Disease control of the plant bacterial pathogens causing citrus canker and rice blight

ABSTRACT

The present invention describes applications and methods (1) to use bacteriophage Cf and its variants to prevent and treat the citrus canker pathogen,  Xanthomonas citri  subsp.  citri;  (2) to engineer recombinant Cf phages that the infectivity is controllable without being harmful to the rest of environment; (3) to engineer and produce recombinant Cf phages with longer storage shelf life; (4) to use Cf phage as a vector for the introduction and insertion of foreign genetic material into  Xanthomonas citri  subsp.  citri.  genome; (5) to use and engineer Xp12 and Xf bacteriophages to inhibit  Xanthomonas oryzae  pv.  oryzae,  the causal agent of the rice blight disease.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 62/016,972 filed, Jun. 25, 2014, the contents of which are incorporated herein by reference in its entirety.

FIELD

The disclosure provides novel genes that encode pesticidal proteins. These proteins and the nucleic acid sequences that encode them are useful in controlling and treating plant bacterial pathogens associated with plant diseases, such as citrus canker and rice blight.

BACKGROUND

Xanthomonas is a genus of Proteobacteria, many of which cause plant diseases that leads to major economic loss. This application describes novel methods using native or genetic engineered bacteriophages to inhibit Xanthomonas infection in the field.

Citrus canker is caused by a bacterial pathogen, Xanthomonas citri subsp. citri (formly X. axonopodis pv. citri, or X. campestris pv. citri), and is one of the most devastating diseases on citrus plants. Infection causes lesions on the leaves, stems, and fruit of citrus trees, including lime, oranges, and grapefruit. Canker significantly affects the vitality of citrus trees, causing leaves and fruit to drop prematurely. A fruit infected with canker is generally too unsightly to be sold.

Citrus canker disease was first recorded in South East Asia in 1827, and it is extremely persistent when it becomes established in an area. Citrus groves have been destroyed in attempts to eradicate the disease. Some areas of the world have eradicated citrus canker and others have ongoing eradication programs, but the disease remains endemic in most areas where it has appeared. Because of its rapid spread, high potential for damage, and impact on export sales and domestic trade, citrus canker is a significant threat to all citrus-growing regions. Many countries like the United States and Brazil are currently suffering from canker outbreaks. The first introduction of citrus canker in Florida was in 1910 on trifoliate rootstock seedlings imported from Japan. The disease spread around the Gulf Coast from Texas to Florida and further north to South Carolina. Citrus canker has been a serious problem in Florida since the last outbreak which began in 1995. This disease is now also present in Japan, South and Central Africa, the Middle East, Bangladesh, the Pacific Islands, some countries in South America. In Florida alone, costs of running eradication program from 1995 through 2005 plus compensation to commercial growers and homeowners for residential citrus destroyed is approaching $1 billion dollars. Under the current citrus canker quarantine instituted by USDA/APHIS at the end of 2013, the interstate movement of citrus plants and plant parts other than fruit remains prohibited in the US. (Gottwald, 2000).

Copper-based products have been to be an effective means of controlling citrus canker. However, copper has been shown to stimulate the growth of mite populations in citrus tree (Mao et. al. 2011). Additionally, copper buildup on the citrus groves and copper-resistant pathogens are also potential problems. Developing a new science-based approach for managing and eradicating citrus canker in the field is emergent and critical.

Bacteriophage (or called “phage” in this application interchangeably) is a naturally occurring virus that that infects and replicates within bacteria. The replication of a bacteriophage may have a “lytic cycle” or a “lysogenic cycle”, and a few viruses are capable of carrying out both. With lytic phages, bacterial cells are broken open (lysed) and destroyed after immediate replication of the phage. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. Lytic phages have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe, as well as in France. They are seen as a possible therapy against multi-drug-resistant strains of many bacteria. In contrast, the lysogenic cycle does not result in immediate lysing of the host cell. Lysogenic viral genome will integrate with host DNA and replicate along with it fairly harmlessly, or may even become established as a plasmid. The virus remains dormant until host conditions deteriorate, then the endogenous phages (known as “prophages”) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is reproduced in all of the cell's offspring.

A novel filamentous bacteriophage Cf was first isolated from citrus canker pathogen, Xanthomonas citri subsp. citri, by Dai et al. in Taiwan (Dai, et al., 1980) and has been studied for decades. Cf bacteriophage and its variants have several unique characteristics with its host bacteria, making it become a novel reagent to prevent and inhibit citrus canker disease in this application:

(1) Unlike other filamentous single-stranded DNA bacteriophages that replicate independently and separately from the host genomic DNAs, two Cf phage variants (Cf1t and Cf16) can integrate their DNAs into its Xanthomonas host genome (Kuo et al., 1987a, Dai, et al, 1988). Only one copy of Cf1t or Cf16 DNA was stably integrated per host chromosome and become lysogenic, which they replicate together with host genome during bacteria growth (Dai et al., 1987; Kuo et al., 1987b).

(2) In contrast to Cf16, one Cf variant called Cf16-v1 was exceedingly unstable during the integration in host DNA genome, and it produces clear plaques and kills host cells. Only 4% of the infected bacterial cells, rather than 95% as in the case of Cf16, retained the phage genome (Dai, et al, 1987).

(3) The integration region of Cf16-v1 phage and host attachment sites (attP and attB) shared an identical 15-bp “core,” 5′-TATACATTATGCGAA-3′. The sequence characteristics indicate that insertion of Cf16-v1 into host genome was accomplished by a site-specific recombination mechanism (Dai et al., 1988).

(4) A virulent Cf variant called Cf1c, was derived from of Cf1t and has been sequenced. The phage yield is higher than Cf1t, and the infected host bacteria growth is drastically reduced (Kuo et al., 1991). Sequence data revealed mutations located in the upstream region of an open reading frame (ORF165) which might encode a 18.2-kDa protein. When the ORF165 in Cf1t was disrupted, this recombinant phage can kill bacteria and form clear plaques (Shieh, et al., 1991).

(5) After Xanthomonas host genome was integrated with Cf1t phage DNA, the bacteria is “immuned” and is no longer susceptible to another Cf phage infection. A variant, Cf1tv (or Cf-tv1), that only lyses cell and its DNA never integrates into host DNA genome, was also isolated. Cf1tv has been proven able to superinfect the immuned bacteria that already contain Cf inside. After infected with Cf1tv, bacterial cell division was seriously affected and finally stopped (Kuo et al., 1994). The region that causes this superinfection activity of Cf1tv and similar variant Cf-tv2 has also been mapped (Wang et al., 1999; Cheng et al., 1999).

A Cf phage variant named XacF1 that shares 99% sequence homology with Cf1c was also isolated from Xanthomonas citri and reported in Japan in July 2014 (Ahmad, et al., 2014). Infection by XacF1 phage caused several physiological changes to the bacterial host cells, including lower levels of extracellular polysaccharide production, reduced motility, slower growth rate, and dramatic reduction in virulence (Ahmad, et al., 2014) (FIG. 17).

Despite that bacteriophages have been used as a tool to kill bacteria in several studies and patents (U.S. 2010/0068185 A1, 3/2010; U.S. Pat. No. 2007/0292395 A1, 12/2007), the specific tool toward to citrus canker disease is unavailable to date. The novel properties make Cf phage and its variants described above become powerful reagents to eradicate citrus canker pathogen in the field.

During our work surveying new phages that can potentially inhibit citrus canker pathogen, a new prophage Cf2 is also identified that integrates within genomic sequence of Xanthomonas citri (strain Aw 12879) and is described in this invention. Cf2 phage DNA integrates within genomic sequence of citrus canker pathogen Xanthomonas citri (strain Aw 12879) and exists as a prophage. The genome of Cf2 prophage is 6453 nucleotide in size, smaller than Cf1c (7303 nucleotide) or Cf variant XacF1 (7325 nucleotide). Cf2 shares 88% nucleotide sequence homology and has similar gene organization with other filamentous phage phiLf, indicating that Cf2 is also a lysogenic ssDNA phage that belongs to Inoviridae family (FIG. 13A).

Sequence analysis reveals that Cf2 phage contains 12 putative protein-coding genes, including Cf1cp7-like protein, chloride channel EriC, Zot protein gI, minor coat protein gVI, gIX and A, major coat protein B, ssDNA binding protein gV, RstA-type replication protein, 2 hypothetical proteins, and a protein similar to Cf 18.2 kDa (ORF165) protein. Importantly, Cf2 shares only very limited sequence homology (less than 10%) with Cf or its variant XacF1 phage, indicating that it is a new lysogenic phage that infects citrus canker pathogen X. citri.

Unlike Cf or phiLf phage, Cf2 phage contains RstA-type replication initiation protein (FIG. 13A). RstA-type replication initiation protein is also found in other lysogenic phages such as phiSMA6, phiSMA7, and phiSMA9 phages that infect bacterial host Stenotrophomonas maltophilia and Xylella fastidiosa related to Xanthomonas. It suggests that Cf2 may require different host factors for its replication. The amino acid sequence of major coat protein B of Cf2 phage shares 76% identity to phiLf phage (FIG. 13B). Characterization of minor coat protein A of Cf2 exhibits novel chimeric properties. Its C-terminus amino acid 303 to 382 is 73% identical to phiLf coat protein A. However, N-terminal amino acid 3 to 211 of Cf2 coat protein A shares 28% identity to Cf homologue (FIG. 12B). Since host specificity of Cf or phiLf phage for X. citri and X. campestris is mediated by minor coat protein A (Yang and Yang, 1997), this result also suggests that the determinant domain of coat protein A for phage-host specificity is located at its N-terminus.

Cf2 phage DNA also integrates into host bacterial genome at attP sequence located at the C-terminus of 18.2 kDa protein similar to Cf ORF165. Similar location of attP sequence is also found in other lysogenic ssDNA filamentous phages, such as Cf1c, XacF1, phiLf, and Xf (FIG. 14). However, Cf2 contains a different 13-bp core attP sequence (5′-TAATTATGTCAAA-3′) in comparison to 15-bp core attP sequence (5′-TATACATTATGCGAA-3′) identified in other lysogenic filamentous phages (FIG. 14).

The region of DNA sequence and organization that causes superinfection activity of Cf1tv and Cf-tv2 is located at the upstream sequence of ORF165 that contains a predicted promoter region encoding cM1 and cM2 transcripts (FIG. 3, FIG. 5B, FIG. 15) (Cheng et al., 1999). The 49 base pair deletion of Cf-tv2 is upstream of ORF 165. The T in the start codon of ORF165 is mutated of the single base substitution to A in Cfltv. This T is also located next to −10 consensus TATA box of a predicted promoter for cM1 transcript (FIG. 5B). In addition, the virulent Cf variant XacF1 also contains G to A substitution at this −10 TATA box, which is one nucleotide downstream to Cf1tv mutant (Ahmad, et al., 2014) (FIG. 15). These results lead to the conclusion that this predicted promoter is the determinant for phage immunity.

Cf2 and Cf phage shares almost no sequence homology in their entire genome except the starting 58 nucleotides of cM2 transcript of Cf is 95% identical to Cf2. The −35 and −10 consensus sequences are also found in the upstream of ORF162 in Cf2 (FIG. 15), indicating that the critical region for phage immunity is also conserved in Cf2. These findings suggest that Cf2 can be also engineered into a virulent variant as a bio-control reagent against citrus canker pathogen.

This invention describes the applications of Cf and Cf2 and their variant bacteriophages to infect and kill Xanthomonas citri subsp. citri, including producing Cf and Cf2 phages in an industrial laboratory and used in citrus groves.

The infectivity of Cf phages requires its minor coat protein A (Yang and Yang, 1997). When Cf genome loses its coat protein A gene, it no longer produces infectious phage particles, and becomes harmless to its bacterial host. Loss of infectivity in the coat protein A-mutated Cf phage can be completely rescued in the presence of minor coat protein A when co-expressed by the other vector. This provides a great system to generate recombinant Cf phages that cannot infect other new bacteria after killing the first bacterial cell they encounter. Unlike other bacteriophage patents in effect so far, this invention also includes a new method to make recombinant Cf phages as “controllable” reagents and do not spread out in natural environment after treating citrus canker in citrus groves. This method will generate bacteriophages as much more secure anti-bacterial reagents without being harmful to the rest of environment.

In taxonomy, Cf phage belongs to Inoviridae family, in which a group of filamentous phages (e.g., Xf, fd, If1,Ike, Pf1, Pf3, phiLF, etc.) has been characterized for their biochemical and biophysical properties (reviewed in Day et al., 1988). For examples, Xf phage was isolated from rice bacterial blight disease pathogen Xanthomonas oryzae or phiLF from Xanthomonas campestris (Kuo et al., 1969; Tseng, et al., 1990; Weng and Tseng, 1994). Compared to Cf, both Xf and phiLF phage particles are relatively stable. The Xf phage particles are resistant to treatment with nucleases or proteases and also maintain its full infectivity in phosphate buffer (pH 7.0) when stored in −15° C. for one year (Kuo et al., 1969). phiLF phage particles are stable for 6 months at 4° C. and keep 100% infectivity even at 80° C. for more than 10 minutes (Tseng et al., 1990). These stable properties of the coat proteins also has made Xf phage an excellent model virus in many biophysical studies previously (Lin et al, 1971; Martin et al., 1974; Wiseman and Day, 1977; Chen, et al., 1980; Thomas and Day, 1981; Casadevall and Day, 1982; Thomas et al., 1983; Marzec and Day, 1983; Marzec and Day, 1988; Thomas et al., 1988; Marzec and Day, 1994). We take advantage of the fact that Cf and Xf phages can be packed with the coat protein from each other (Yang and Yang, 1997). This invention also includes a method engineering a recombinant Cf phage with the coat proteins from other members of Inoviridae family (Xf, phiLF, fd, If1, Ike, Pf1, Pf3, Cf2 etc.) to enhance the stability of Cf phage particles for further application.

Xanthomonas oryzae pv. oryzae causes rice bacterial blight (BB) disease which is one of the most important diseases of rice in most of the rice growing countries (Nino-Liu, et al., 2006). Rice blight has high epidemic potential and is destructive to high-yielding cultivars in both temperate and tropical regions especially in Asia. Its occurrence in the 70s in Africa and the Americas has led to concerns about its transmission and dissemination. X. oryzae pv. oryzae can destroy up to 80 percent of a crop if the disease develops early. Even if it develops late, it can nonetheless severely diminish the quality and yield of the grain. Bacterial leaf blight is a prevalent and destructive disease that affects millions of hectares throughout Asia. In Japan alone, annual losses are estimated to be between 22,000 and 110,000 tons. In the Philippines, susceptible varieties lose up to 22.5% of the total harvest during wet seasons and up to 7.2% in the dry season. In resistant crops, these numbers are, respectively, 9.5% and 1.8% (Exconde, 1973).

Research on bacterial blight of rice was commenced in Japan as early as in 1901, and the efforts were focused mainly on ecological studies and chemical control. Since then, significant gains have been made in understanding BB through analysis of the interactions between X. oryzae pv. oryzae and rice at many levels, including studies focused on the epidemiology, population biology, physiology, cell biology, biochemistry, and molecular genetics of the host pathogen interaction. Bacterium oozes from leaf lesions and is spread by wind or rain, especially when strong storms occur and cause wounds to plants. X. oryzae has a wide host range that includes a rice cutgrass called Leersia sayanuka which acts as alternative host for the bacterium. The presence of L. sayanuka, is also key to the spread of disease because it is a naturally growing weed usually found around patties and has the ability to be infected by the bacterium and spread the bacterium through a rice patty.

One virulent bacteriophages Xp12, was isolated from Xanthomonas oryzae pv. oryzae in the irrigation water in a rice field in Taiwan in 1968 (Kuo et al., 1968). Xp12 phage is distinguished from other known phages isolated so far because it processes DNA in which all the cytosine residues are completely replaced by 5-methylcytosine (Kuo et al. 1968; Ehrlich et al. 1975). This 5-methylcytosine substitution has made Xp12 an important tool for studying the mechanism of naturally occurring DNA methylation in molecular biology field for decades (Kuo and Tu 1976; Ehrlich et al. 1977; Wang and Ehrlich, 1982; Kuo et al., 1982). Xp12 has been also a model system for analyzing the digestion ability of restriction endonucleases (McClelland and Nelson 1991).

The other bacteriophage, Xf, is a filamentous phage also able to infect rice blight but not inhibit bacterial growth (Kuo, et al., 1969). Xf phage invades the host cells with its coat protein (Kuo and Lin, 1976). However, the sequence information of Xf phage genome has not been reported. We also identify the complete nucleotide sequence of Xf phage genome. In an aspect, the disclosure applies the unique features of Xp12 and Xf phage to engineer these phages and to the control the rice blight disease in the field.

Xanthomonas campestris pv. citri was reclassified as X. axonopodis in 1995. In 2006, the species designations for pv. citri and malvacearum were revised to X. citri and these pathovars are now referred to as subspecies Xanthomonas campestris.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: (A) The plague morphology of bacteriophage Cf (left) and Cflt (right). (B) Electron micrograph of bacteriophage Cflt, stained with 2% phosphotungstic acid is described (Kuo et al., 1987).

FIG. 2. (A) The Cf16-v1 attachment site was localized to the unique PstI-KpnI fragment by restriction mapping. HindIII cleaves the circular Cf16-v1 RF into two fragments of approximately 5.8 and 1.8 kb, respectively. Three lysogen HindIII fragments with a size of 1.8, 3.0 (H′), and 4.3 (H) kb, respectively, hybridize to the Cf16 probe. In the diagram, the sum of A and B should equal 5.8 kb, while the sum of C and D should equal the host HindIII fragment that contains the Cf16-v1 attachment site. The size of this fragment is calculated as H+H′−A−B=1.5 kb. Solid triangle: center of the attachment site (drawn in opposite orientation in the phage and the host chromosome). (B) Nucleotide sequence of Cfl6-vl in the vicinity of the phage attachment site. The common core sequence is underlined. Inverted repeats, potential recognition sequences for a site-specific recombination enzyme, are designated by arrows. Repeated sequences, potential binding site of another protein factor, are designated by dashed lines. Two orientations of these sequences are indicated. Sequences are numbered with bp zero assigned to the center of the 15-bp common core sequence. (C) Nucleotide sequence of Xanthomonas citri subsp. citri in the vicinity of the Cfl6-v1 attachment site. Designations used are the same as in (B) (Dai et al., 1988).

FIG. 3. (A) Map of Cf RF DNA showing the location of genes and cleavage sites of the restriction endonucleases. Except for ORF165, transcription of all the investigated genes proceeds clockwise. (B) Mutation sites on the Cf-tv2 mutant. (a) DNA sequencing gel showing the mutation in Cf-tv2. (b) Location of the Cf-tv2 mutation on the cf genome. The 49 base pair deletion of Cf-tv2 is shown in boldface type. The amino acid sequence of ORF 165 is shown in the one-letter code. attP indicates the attachment site for integration in the phage. The T in the start codon of ORF165 represents the mutation of the single base substitution in the virulent mutant, Cfltv (labeled as Cf-tv1 in the figure) (Cheng et al., 1999).

FIG. 4. Cell division of Cfltv-infected Xanthomonas citri cells. Using a microculture technique, cells were observed by light microscope after 16 hour incubation at 28° C., except for a few bacteria which divided slightly slower than the normal-dividing cells and would finally recover to become normal-dividing cell type. (A) Unchanged cells division, (B) infected cells (arrow) are still undivided. The respective culture contains some dividing cells, too. The respective time course of change in cell type over 12 hour incubation period is given in (C) and (D). (C) Uninfected culture, (D) cultures infected with Cfltv. ● Normal-dividing cell type, ▴ slow-dividing cell type, ◯ non-dividing cell type. (Kuo, et al, 1994).

FIG. 5. Primer extension to detect the transcription start sites. (A) Detection of the 5′ end of cMa (Left). The four lanes of dideoxy sequencing reactions (C, T, A, G) using the same primer (5′-CAGGATCGAATATGGATGCACGGTGTA-3′) as in the primer extension reaction are shown. The arrow indicates the 5′ end of the cM1 transcript at G5629. (Right) Detection of the 5′ end of cM2. The four lanes of dideoxy sequencing reactions (C, T, A, G) using the same primer (5′-TGACAGAGAGGACAGTGAAAACTATAC-3′) as the primer extension reaction are shown. The arrow indicates the 5′ end of the cM2 transcript at C5693. (B) Nucleotide sequence upstream of cM1 and cM2 RNAs. The translational start site and the amino acid sequence of ORF 165 in the one letter code are shown. The −35 and −10 consensus sequences of a predicted promoter region are underlined. The big arrows indicate the transcriptional start sites of cM1 and cM2. The 49 base pair deleted in cf-tv2 are shown in boldface type. In (A): lane 1, uninfected Xanthomonas; lane 2, Xanthomonas infected with cf; and lane 3, Xanthomonas infected with cf-tv2 (Cheng et al, 1999).

FIG. 6. Application and generation of Cf-type phages to inhibit citrus canker disease. (A) Cf-M phages are generated by treating Cf-type phages with chemical mutagens that cause variety of gene mutations (orange dots). (B) Cf-Super phages contain mutations nearby or within ORF165 region in RF DNA of Cf-type phages. Arrows indicate the transcriptional start sites of cM1 and cM2 in FIG. 5B. Cf-Super phages are able to infect both uninfected X. citri or bacteria that are previously infected by other Cf-type phages and immuned. Cf-Super phages kill X. citri by lysis of bacteria, and new phages are released to infect more bacteria in a lesion of citrus canker. (C) Summary of the process flowchart of generation and application of Cf-type phages in this patent. Mutated Cf-type phages (A) are used to infect X. citri, or (B) recombinant RF DNAs of Cf-Super are electroporated in X. citri cells. After propagating in X. citri cells, Cf-type phages are harvested and purified from the growth medium. Infectivity and quality control of Cf-type phages are assayed, and phage particles are aliquoted and stored in a lab. In an orange grove, Cf-type phages are sprayed or misted on the citrus trees for field tests. Different Cf-type and variants phages are screened for the control of X. citri with better pathogen inhibition effect than others. Cf-type phages with the greatest inhibitory effects on citrus canker disease are selected for the large-scale production and commercial use.

FIG. 7. Generation of a controllable “single-shot infectious” Cf-type (SS-iCf) phage in this patent. Component A is a plasmid DNA that contains coat protein A gene of Cf-type phage and an essential nutrition gene X. Component B is a recombinant Cf-type RF DNA which the coat protein A gene is replaced by a nutrition gene Y. Component A and B are electroporated together into X. citri mutants lack of both nutrition genes X and Y, then bacteria are grown in a selected nutrition medium to produce SS-iCf phages. SS-iCf phages can infect and kill X. citri cells by the lysis of bacterial cells. Because the genome of SS-iCf phages do not contain the coat protein A gene essential for infectivity, SS-iCf phages cannot propagate into new progeny phages and spread in the filed anymore after being used.

FIG. 8. Generation of recombinant Cf-type phages to improve the storage shelf life. (A) The XC DNA fragments encoding coat proteins from other inoviruses are cloned into RF DNAs of Cf-type phages to replace the major coat protein B gene. The Cf-type RF DNAs containing XC fragments are electroporated into X. citri bacteria and amplified. Cf-XC phage particles are harvested from the medium. (B) Generation of the controllable SS-iCf-XC phages. Component C is a plasmid containing XC DNA fragments and an essential nutrition gene X. Component D is recombinant Cf-type RF DNA which the major coat protein B gene is replaced by a DNA fragment of a nutrition gene Y. Component E is recombinant Cf-type RF DNA with an TA insertion (orange dot) that abolishes the expression of major coat protein B. The mixture of “Component C+D”, or “component C+E”, respectively, is electroporated into X. citri bacteria mutant lack of nutrition genes X and Y. X. citri cells are grown in a selected nutrition medium. SS-iCf-XC phage particles are harvested from the medium. Because the genome of SS-iCf-XC phages do not contain a functional coat protein B gene, SS-iCf-XC phages cannot produce new progeny phages in the filed after infecting and killing X. citri bacteria.

FIG. 9. Generation of Cf-type phages able to kill X. citri bacteria. (A) A DNA fragment encoding a toxic gene able to kill X. citri bacteria is cloned into RF DNAs of Cf-type phages. The recombinant Cf-type RF DNAs containing a toxic gene (brown dots) are electroporated into X. citri bacteria and amplified. Cf-killer phage particles are harvested from the medium. (B) Generation of the controllable SS-iCf-killer phages. Component A is a plasmid DNA that contains coat protein A gene of Cf-type phage and an essential nutrition gene X. Component J is recombinant Cf RF DNAs which contain a toxic gene, and the coat protein A gene is replaced by nutrition gene Y. Component A and J are electroporated together into X. citri mutants lack of both nutrition genes X and Y, then bacteria are grown in a selected nutrition medium to produce SS-iCf-killer phages. SS-iCf-killer phages can infect and kill X. citri cells. Because the genome of SS-iCf-killer phages do not contain the coat protein A gene essential for infectivity, SS-iCf phages cannot propagate into new progeny phages and spread in the filed anymore after being used.

FIG. 10. Generation and application of a Cf-Shuttle vector that can carry a foreign gene that integrates into X. citri host DNA genome. Component A is a plasmid DNA that contains coat protein A gene of Cf-type phage and an essential nutrition gene X. Component K (Cf-Shuttle vector) contain a DNA fragment encoding a foreign gene to replace coat A gene in RF DNA of Cflt phage. The mixture of Component K and component A are electroporated together into X. citri mutants lack of nutrition gene X. Cells are grown in a selected nutrition medium. Cf-shuttle vector will integrate into X. citri host genome and replicates with bacteria. With Component A, Cf-Shuttle phages can be also generated and released into medium.

FIG. 11. Application and generation of XP12 variant phages to inhibit rice blight disease. (A) Summary of the process flowchart of generation and application of XP12 variant phages in this patent. XP12 variant phages are generated either by treating XP12 phages with chemical mutagens, or XP12 DNA is mutated by PCR. After propagating in X. oryzae cells, XP12 phages are harvested and purified from the growth medium. Infectivity and quality control of XP12 phages are assayed, and phage particles are aliquoted and stored in a lab. In a rice field, XP12 variant phages are sprayed or misted in field tests to screen for the control of X. oryzae with better pathogen inhibition effect than others. XP12 phages with the greatest inhibitory effects on rice blight are selected for the large-scale production and commercial use. XP12 variant phages are able to infect and kill X. oryzae by lysis of bacteria, and new progeny XP12 phages are released to infect more bacteria in a lesion of rice blight. (B) Generation of a controllable SS-iXP12 phage in this patent. Component L is a plasmid DNA that contains coat protein and RNA polymerase genes of XP12 phage and an essential nutrition gene X. Component M is a recombinant XP12 DNA, which the coat protein and RNA polymerase gene are replaced by nutrition gene Y and Z, respectively. Component L and M are electroporated together into X. oryzae mutant lack of both nutrition genes X, Y, and Z. Bacteria are grown in a selected nutrition medium to produce SS-iXP12 phages. SS-iXP12 phages can infect and kill X. oryzae cells by the lysis of bacterial cells. Because the genome of SS-iXP12 phages do not contain the coat protein and RNA polymerase gene, SS-iXP12 phages cannot propagate into new progeny phages and spread in the filed anymore after being used.

FIG. 12. Application and generation of Xf variant phages to inhibit rice blight disease. (A) Summary of the process flowchart of generation and application of Xf variant phages in this patent. Xf variant phages are generated either by treating Xf phages with chemical mutagens, or Xf RF DNA is mutated by PCR and electroporated into X. oryzae. After propagating in X. oryzae cells, Xf phages are harvested and purified from the growth medium. Infectivity and quality control of Xf phages are assayed, and phage particles are aliquoted and stored in a lab. In a rice field, Xf variant phages are sprayed or misted in field tests to screen for the control of X. oryzae with better pathogen inhibition effect than others. Xf variant phages with the greatest inhibitory effects on rice blight are selected for the large-scale production and commercial use. Xf variant phages are able to infect and kill X. oryzae by lysis of bacteria, and new progeny Xf phages are released to infect more bacteria in a lesion of rice blight. (B) Generation of a controllable SS-iXf phage in this patent. Component N is a plasmid DNA that contains coat protein B gene of Xf phage and an essential nutrition gene X. Component O is a recombinant Xf DNA, which the coat protein B gene is replaced by nutrition gene Y. Component N and O are electroporated together into X. oryzae mutant lack of both nutrition genes X and Y. Bacteria are grown in a selected nutrition medium to produce SS-iXf phages. SS-iXf phages can infect and kill X. oryzae cells by the lysis of bacterial cells. Because the genome of SS-iXf phages do not contain the coat protein B gene, SS-iXf phages cannot propagate into new progeny phages and spread in the filed anymore after being used.

FIG. 13. Characterization of Cf2 phage genome isolated from X citri. (A) Comparison of genome organization of Cf2 and phiLf phage. Direction of Cf1cp7-like protein and Cf 18.2 kDa/ORF165-like protein transcripts is opposite to other ORFs. (B) (Upper) Comparison of amino acid sequences of major coat protein B of Cf2 and phiLf. (Middle and bottom) Comparison of amino acid sequences of minor coat protein A between Cf2 and Cf (middle), or between Cf2 and phiLf (bottom).

FIG. 14. Nucleotide sequence in the vicinity of the phage attachment site (attP) identified in lysogenic phages (Cf1c, XacF1, Cf2, phiLF, and Xf,). The core attP sequence is underlined. Asterisk shows core attP sequences different from 5′-TATACATTATGCGAA-3′ in Cf2 phages. All attP sites are located at the C-terminus of an ORF encoding a protein similar to Cf1cp8 (18.2 kDa protein, or ORF165 in FIG. 3). Amino acid sequence and number of ORF165 homologue of each phage is shown.

FIG. 15. The determinant sequences of phage immunity in Cf1c, XacF1, and Cf2 phage. The ORF165 is shown in boldface type. The −35 and −10 consensus sequences of a predicted promoter region are underlined. The boxes indicate the transcriptional start sites of cM1 and cM2. The boundary of the 49 base pair deletion of Cf-tv2 is shown by the arrows. The A in the −10 TATA box represents the mutation of the single base G to A substitution in the virulent Cf variant XacF1. The 58-nucleotide sequence in Cf2 genome with 95% homology with Cf is located upstream of G labeled in italic.

FIG. 16. Agarose gel electrophoresis of Cf and Cf2 phage DNA. Synthetic DNA fragments of full-length 7.3 kb genomic DNA of Cf phage (lane 1-8) were ligated and subcloned into a kanamycin-resistant plasmid vector. Plasmids were digested with EcoRI and analysed in 1% TAE agarose gel. Synthetic DNA fragments of full-length 6.4 kb genomic DNA of Cf2 phage (lane 9).

FIG. 17. Lesions on detached lemon leaves inoculated with cells of Xanthomonas citri Xac MAFF301080. (A) Canker symptoms that had developed on leaves 1,2, 3, and 4 week spost-infection by the needle-pricking method. Leaves were inoculated with uninfected cells (upper panels) or Cf strain XacF1-infected cells (lower panels). Leaf are as shown by a square were examined by photomicroscopy and the microscopic images are shown under each corresponding leaf. Characteristic canker lesions occurred with uninfected cells, while no obvious cankers developed on XacF1-infected cells. (B) Comparison of the size of lesions formed on lemon leaves. (C) Lesions formed on lemon leaves by infiltration of bacterial cells. Uninfected MAFF301080 cells were applied to two areas of the leaf (left half of the abaxial side), and XacF1-infected cells were similarly applied to the right side (upper panels). Lesions on the axial side are also shown in lower panels. Lesions on both lower and upper surfaces of leaves inoculated with the uninfected cells showed severe symptoms, expanding with time. No lesions formed on either surface of the leaves infected with XacF1-infected cells (Ahmad et al., 2014).

DETAILED DESCRIPTION

In an aspect, the disclosure provides for a composition, seed, plant, vector, or construct comprising a sequence described herein.

Proteins and the nucleic acid sequences that encode them described herein are useful in controlling and treating plant pathogens associated with plant bacterial pathogens, such as citrus canker and rice blight.

In another aspect, the disclosure provides for methods of utilizing a sequence described herein to treat or reduce pest activity. In yet another aspect, the disclosure provides for methods of utilizing a sequence described herein to treat or reduce pest activity, for example, pest activity in Xanthomonas, for example, X. albilineans, X. arboricola sp., X. axonopodis sp., X. bromi, X. campestris spp., X. cassavae, X. citri, X. codiaei, X. cucurbitae, X. cynarae, X. fragariae, X. fuscans, X. gardneri, X. hortorum, X. hyacinthi, X. melonis, X. oryzae sp., X. pisi, X. populi, X. sacchari, X. theicola, X. translucens sp., X. vasicola, X. vesicatoria, X. spp., but also including other bacteria such as Xylella fastidiosa, Pseudomonas and Enterobacteriaceae infection.

In an aspect, the disclosure provides for a method of inhibiting, reducing, or treating infection or infestation of citrus canker, rice blight, black rot, and/or bacterial leaf spot, leaf spot disease, sugarcane leaf scald, and other Xanothomonas or Xylella infection.

In an aspect, nucleotide sequences encoding the proteins of the present invention include the sequence set forth in SEQ ID NO:1-2, 24, 25, 26 and variants, fragments, and complements thereof. In another aspect, proteins of the present invention are encoded by a nucleotide sequence sufficiently identical to the nucleotide sequence of SEQ ID NO:1-2, 24, 25, 26 or the pesticidal proteins are sufficiently identical to the amino acid sequence set forth in SEQ ID NO:3-23, 27-62. By “sufficiently identical” is intended an amino acid or nucleotide sequence that has at least about 50%, 60%, or 65% sequence identity, about 70% or 75% sequence identity, about 80% or 85% sequence identity, about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater sequence identity compared to a reference sequence using one of the alignment programs described herein using standard parameters. One of skill in the art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like.

In another aspect, the disclosure provides for a protein or polypeptide having an amino acid sequence that is at least about 50%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98% or about 99% identical to the amino acid sequence of any of SEQ ID NO:3-23, 27-62. Variants also include polypeptides encoded by a nucleic acid molecule that hybridizes to the nucleic acid molecule of SEQ ID NO:3-23, 27-62 or a complement thereof, under the condition that permit a formation of a nucleic acid duplex at the temperature from 20° C.-29° C. below the melting temperature of the nucleic acid duplex in the hybridization and washing solution with 0.165-0.33 molar concentration of sodium chloride . Variants include polypeptides that differ in amino acid sequence due to mutagenesis. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the desired biological activity of the native protein, that is, retaining pesticidal activity. In some embodiments, the variants have improved activity relative to the native protein.

As described in the sequence listing, SEQ ID 3 comprises a Cf1cp1, ssDNA-binding protein “=pV of Ff phage” and is encoded by SEQ ID 1: nucleotide number 7087-7308; 1-75.

As described in the sequence listing, SEQ ID 4 comprises Cf1cp2, B coat protein and is encoded by SEQ ID 1: nucleotide number 313-585.

As described in the sequence listing, SEQ ID NO: 5 comprises Cf1cp3, minor coat protein A=pIII of M13/Fd phage and encoded by SEQ ID 1: nucleotide number 662-1918.

As described in the sequence listing, SEQ ID NO: 6 comprises Cf1cp4, ATPase, zonular occludens toxin, able to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers=pI in F1 phage, which is encoded by SEQ ID 1: nucleotide number 2481-3647.

As described in the sequence listing, SEQ ID 7 comprises Cf1cp5, conjugal transfer protein TrbP/Trax and is encoded by SEQ ID 1: nucleotide number 3647-4294.

As described in the sequence listing, SEQ ID NO: 8 comprises Cf1cp6, DUF 4124, which is a potential secreted protein and encoded by SEQ ID 1: nucleotide number 4310-4702.

As described in the sequence listing, SEQ ID 9 comprises Cf1cp7, similar to ORF110 of Xanthomonas campestris and is encoded by SEQ ID 1: nucleotide number 4710-5123.

As described in the sequence listing, SEQ ID 10 comprises Cf1cp8, ORF165, 18.2 kDa protein, for virus immunity of Xanthomonas citrus and is encoded by SEQ ID 1: nucleotide number 5120-5620.

As described in the sequence listing, SEQ ID 11 comprises Cf1cp9, a probable site-specific integrase; similar to Replication-associated protein G2P=pII in M13/f1 phage and is encoded by SEQ ID 1: nucleotide number 6057-7090.

As described in the sequence listing, SEQ ID NO: 12 comprises ORF165, and is encoded by SEQ ID 1: nucleotide number 5120-5620.

As described in the sequence listing, SEQ ID NO: 27 comprises XacF1 ORF1, and is encoded by SEQ ID 24: nucleotide number 1-1080.

As described in the sequence listing, SEQ ID NO: 28 comprises XacF1 ORF2, and is encoded by SEQ ID 24: nucleotide number 1077-1373.

As described in the sequence listing, SEQ ID NO: 29 comprises XacF1 ORF3, and is encoded by SEQ ID 24: nucleotide number 1405-1605.

As described in the sequence listing, SEQ ID NO: 30 comprises XacF1 ORF4, and is encoded by SEQ ID 24: nucleotide number 1611-1868.

As described in the sequence listing, SEQ ID NO: 31 comprises XacF1 ORF5, and is encoded by SEQ ID 24: nucleotide number 1928-1996.

As described in the sequence listing, SEQ ID NO: 32 comprises XacF1 ORF6, and is encoded by SEQ ID 24: nucleotide number 996-3474.

As described in the sequence listing, SEQ ID NO: 33 comprises XacF1 ORF7, and is encoded by SEQ ID 24: nucleotide number 3474-3791.

As described in the sequence listing, SEQ ID NO: 34 comprises XacF1 ORF8, and is encoded by SEQ ID 24: nucleotide number 3788-4954.

As described in the sequence listing, SEQ ID NO: 35 comprises XacF1 ORF9, and is encoded by SEQ ID 24: nucleotide number 4954-5601.

As described in the sequence listing, SEQ ID NO: 36 comprises XacF1 ORF10, and is encoded by SEQ ID 24: nucleotide number 5617-6009.

As described in the sequence listing, SEQ ID NO: 37 comprises XacF1 ORF11, and is encoded by SEQ ID 24: nucleotide number 6047-6430.

As described in the sequence listing, SEQ ID NO: 38 comprises XacF1 ORF12, and is encoded by SEQ ID 24: nucleotide number 6427-6885.

As described in the sequence listing, SEQ ID NO: 39 comprises XacF1 ORF13, and is encoded by SEQ ID 24: nucleotide number 7015-7203.

As described in the sequence listing, SEQ ID NO: 40 comprises Cf2 similar to Cf1cp7 protein, and is encoded by SEQ ID 25: nucleotide number 98-424.

As described in the sequence listing, SEQ ID NO: 41 comprises Cf2 chloride channel EriC protein, and is encoded by SEQ ID 25: nucleotide number 491-802.

As described in the sequence listing, SEQ ID NO: 42 comprises Cf2 Zot protein, and is encoded by SEQ ID 25: nucleotide number 812-2156.

As described in the sequence listing, SEQ ID NO: 43 comprises Cf2 minor coat protein, and is encoded by SEQ ID 25: nucleotide number 2158-2478.

As described in the sequence listing, SEQ ID NO: 44 comprises Cf2 minor coat protein A, and is encoded by SEQ ID 25: nucleotide number 2489-3682.

As described in the sequence listing, SEQ ID NO: 45 comprises Cf2 major coat protein B, and is encoded by SEQ ID 25: nucleotide number 3817-3945.

As described in the sequence listing, SEQ ID NO: 46 comprises Cf2 minor coat protein, and is encoded by SEQ ID 25: nucleotide number 3972-4223.

As described in the sequence listing, SEQ ID NO: 47 comprises Cf2 ssDNA binding protein, and is encoded by SEQ ID 25: nucleotide number 4227-4505.

As described in the sequence listing, SEQ ID NO: 48 comprises Cf2 phage replication protein RstA, and is encoded by SEQ ID 25: nucleotide number 4484-5371.

As described in the sequence listing, SEQ ID NO: 49 comprises Cf2 conserved protein, and is encoded by SEQ ID 25: nucleotide number 5371-5558.

As described in the sequence listing, SEQ ID NO: 50 comprises Cf2 hypothetical protein, and is encoded by SEQ ID 25: nucleotide number 5728-5952.

As described in the sequence listing, SEQ ID NO: 51 comprises Cf2 18.2 kDa protein, and is encoded by SEQ ID 25: nucleotide number 6080-6468.

As described in the sequence listing, SEQ ID NO: 52 comprises Xf similar to Cf1cp7 protein, and is encoded by SEQ ID 26: nucleotide number 90-473.

As described in the sequence listing, SEQ ID NO: 53 comprises Xf TrbP protein, and is encoded by SEQ ID 26: nucleotide number 645-1292.

As described in the sequence listing, SEQ ID NO: 54 comprises Xf Zot protein, and is encoded by SEQ ID 26: nucleotide number 1294-2484.

As described in the sequence listing, SEQ ID NO: 55 comprises Xf hypothetical protein, and is encoded by SEQ ID 26: nucleotide number 2481-2810.

As described in the sequence listing, SEQ ID NO: 56 comprises Xf minor coat protein A, and is encoded by SEQ ID 26: nucleotide number 2810-4258.

As described in the sequence listing, SEQ ID NO: 57 comprises Xf major coat protein B, and is encoded by SEQ ID 26: nucleotide number 4353-4583.

As described in the sequence listing, SEQ ID NO: 58 comprises Xf ssDNA binding protein, and is encoded by SEQ ID 26: nucleotide number 4802-5098.

As described in the sequence listing, SEQ ID NO: 59 comprises Xf replication initiation protein, and is encoded by SEQ ID 26: nucleotide number 5095-6135.

As described in the sequence listing, SEQ ID NO: 60 comprises Xf hypothetical protein, and is encoded by SEQ ID 26: nucleotide number 6288-6500.

As described in the sequence listing, SEQ ID NO: 61 comprises Xf hypothetical protein, and is encoded by SEQ ID 26: nucleotide number 6500-6685.

As described in the sequence listing, SEQ ID NO: 62 comprises Xf Cf1c 18.2 kDa-like protein, and is encoded by SEQ ID 26: nucleotide number 6771-7205.

It is recognized that DNA sequences of a pesticidal protein may be altered by various methods, and that these alterations may result in DNA sequences encoding proteins with amino acid sequences different than that encoded by a pesticidal protein of the present invention. This protein may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions of one or more amino acids of SEQ ID NO:3-23, 27-62 including up to about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 55, about 60, about 65, about 70, about 75, about 80, about 85, about 90, about 100 or more amino acid substitutions, deletions or insertions.

The skilled artisan will further appreciate that changes can be introduced by mutation of the nucleotide sequences of the invention thereby leading to changes in the amino acid sequence of the encoded pesticidal proteins, without altering the biological activity of the proteins. Thus, variant isolated nucleic acid molecules can be created by introducing one or more nucleotide substitutions, additions, or deletions into the corresponding nucleotide sequence disclosed herein, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Such variant nucleotide sequences are also encompassed by the present invention.

For example, conservative amino acid substitutions may be made at one or more, predicted, nonessential amino acid residues. A “nonessential” amino acid residue is a residue that can be altered from the wild-type sequence of a pesticidal protein without altering the biological activity, whereas an “essential” amino acid residue is required for biological activity. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).

In an aspect, amino acid substitutions may be made in nonconserved regions that retain function. In general, such substitutions would not be made for conserved amino acid residues, or for amino acid residues residing within a conserved motif, where such residues are essential for protein activity. Examples of residues that are conserved and that may be essential for protein activity include, for example, residues that are identical between all proteins contained in an alignment of similar or related toxins to the sequences of the invention (e.g., residues that are identical in an alignment of homologous proteins). Examples of residues that are conserved but that may allow conservative amino acid substitutions and still retain activity include, for example, residues that have only conservative substitutions between all proteins contained in an alignment of similar or related toxins to the sequences of the invention (e.g., residues that have only conservative substitutions between all proteins contained in the alignment homologous proteins). However, one of skill in the art would understand that functional variants may have minor conserved or nonconserved alterations in the conserved residues.

Unless otherwise specified, “a” or “an” means “one or more”. As used herein, the terms “and” and “or” may be used to mean either the conjunctive or disjunctive. That is, both terms should be understood as equivalent to “and/or” unless otherwise stated. As used herein, unless otherwise stated for a particular parameter, the term “about” refers to a range that encompasses an industry-acceptable range for inherent variability in analyses or process controls, including sampling error. Consistent with the Model Guidance of AAFCO, inherent variability is not meant to encompass variation associated with sloppy work or deficient procedures, but, rather, to address the inherent variation associated even with good practices and techniques.

As used herein, the term “coating” means a partial or complete covering that covers at least a portion of a surface, for example a surface of a food, plant, seed or fruit. In one example, a food, plant, seed or fruit may be partially covered with a coating such that only part of the plant is covered, and part of the plant is not covered and is thus exposed. In another example, the plant may be completely covered with a coating such that the entire plant is covered and thus not exposed. Thus a coating may cover from a negligible amount up to the entire surface. A coating can also be coated onto other coatings such that a layering of coatings can be present. For example, a plant can be coated with coating A, and coating A can be coated with coating B, such that coating A and coating B each form a layer.

As used herein, the terms “bacteriophage” and “phage” are used interchangeable and refer to a virus which is lytic or otherwise harmful to bacteria of one or more undesirable strains. Undesirable bacteria may be or may produce compounds which are potentially pathogenic for plants, or may be associated with spoilage, malodor, aesthetic decline, or other deterioration of a food product colonized by the undesirable bacteria. As used herein, “bacterium”, “bacteria” or “target bacterium” refers to an undesirable micro-organism susceptible to infection and lysis, apoptosis, or alternate modes of cell death caused by a bacteriophage. Different strains of bacteriophage may infect different strains of bacteria with different results, or may infect some strains of bacteria but not others.

As used herein, “isolated” will mean material removed from its original environment (e.g., the natural environment in which the material occurs) or liquid culture, and thus is “altered by the hand of man” from its natural environment. Isolated material may be, for example, foreign nucleic acid included in a vector system, foreign nucleic acid contained within a host cell, or any material which has been removed from its original environment and thus altered by the hand of man. Isolated material further encompasses isolated phage or particular bacterial isolates of Xanthomonas citri subsp. citri or Xanthomonas oryzae pv. oryzae, isolated and cultured separately from the environment in which it was located, where these isolates are present in purified compositions that do not contain any significant amount of other bacteriophage or bacterial strains, respectively. As used herein, “significant” will mean an amount of a substance present in the total measured composition, wherein the substance is present in greater than 1% of the total volume or concentration of the composition.

As used herein, “recombinant”, “variants”, and “recombinant variants” will mean genomic materials (nucleotides, DNA, RNA, proteins) are artificially engineered and have the same nucleotide and/or amino acid sequences where one or more residues are added, deleted, or substituted.

As used herein, “colonization” or “colonized” will refer to the presence of X. citri subsp. citri, X. oryzae pv. oryzae X. albilineans, X. arboricola sp., X. axonopodis sp., X. bromi, X. campestris spp., X. cassavae, X. citri, X. codiaei, X. cucurbitae, X. cynarae, X. fragariae, X. fuscans, X. gardneri, X. hortorum, X. hyacinthi, X. melonis, X. oryzae sp., X. pisi, X. populi, X. sacchari, X. theicola, X. translucens sp., X. vasicola, X. vesicatoria, X.spp., Xylella fastidiosa, Pseudomonas and Enterobacteriaceae on a plant, foodstuff or environmental surface without perceptible significant alteration to that plant, foodstuff or surface other than the presence of bacteria. The terms “colonization” and “colonized” stand in contrast to the terms “infection” or “infected” which are commonly understood to require perceptible deleterious alteration as part of their definition. “Colonization” and “colonized” may also refer to the presence of bacteria in or on a plant without perceptible damage, alteration, or disease.

As used herein, “ATCC” will mean the “American Type Culture Collection”, which is located at 10801 University Boulevard, Manassas, Va., 20110-2209, USA.

“Centrifugation”, the name given to separation applications which involve spinning around an axis to produce a centrifugal force, is a way to increase the magnitude of the gravitational field. The particles or materials (such as viruses, phages, DNA etc.) in suspension experience a radial centrifugal force moving them away from the axis of rotation. The radial force generated by the spinning rotor is expressed relative to the earth's gravitational force and herein expressed as “g-force” (with g from “gravitational”).

As used herein, “ORF” will mean an “Open Reading Frame” which is an in-frame sequence of codons that (in view of the genetic code) correspond to or encode a protein or peptide sequence. Two ORFs correspond to each other if the sequences or their complementary sequences encode the same amino acid sequences. An ORF sequence, operably associated with appropriate regulatory sequences, may be transcribed and translated into a polypeptide in vivo. As used herein, “homology” will mean the degree of similarity between two nucleic acids (based on comparison of the chemical structure of the nucleic acids, as expressed by the sequence of nucleotides making up the nucleic acid or biologic function, as determined by whether two nucleic acids of minimum length 500 nucleotides and maximum length 10,000 nucleotides will hybridize to form a double-stranded complex).

As used herein, “purify” will mean a method to generate a macromolecule essentially free of any similar macromolecules that would normally be found with it in nature. In other words, a purified protein is in a composition that contains no more than 1% other protein from the same taxonomic species. A purified composition excludes media components, recipients or other non-contaminating compounds resulting from culturing, processing or formulating the composition.

As used herein, “amplification” will mean the in vitro production of multiple copies of a particular nucleic acid sequence. The amplified sequence is usually in the form of DNA. A variety of techniques for carrying out such amplification are described in a review article (Van Brunt, 1990). Polymerase chain reaction (PCR) is a prototype of nucleic acid amplification, and use of PCR herein should be considered exemplary of other suitable amplification techniques.

A regular method of quantification by culturing and counting includes a technique which is typically referred to as a “plaque assay”. In plaque assays, the phages that are to be quantified are mixed with a known concentration of host bacterial cells and transferred to a liquid (e.g., buffer, mineral salts diluent, or broth). The mixture is then transferred to a semisolid growth medium. The concentration of host cells must be sufficiently great to form a confluent layer, which is typically referred to as a “lawn,” in the semisolid growth medium as the cells grow. During incubation of the phage-bacteria mixture, many of the viable viruses infect host cells. Subsequently, new viruses are produced within infected host cells, which are eventually destroyed, or “lysed,” so that new viruses may be released. The new viruses then attack and eventually lyse cells that are adjacent to host cells from which the new viruses were released. This spread of infection, which continues as long as host cells are metabolizing, results in formation of clear areas, which are typically referred to as “plaques,” in the host cell lawn. The number of viruses that were present in the original mixture is determined by counting the number of plaques that are formed in the host cell lawn. Accordingly, viruses that are quantified by this method are referred to as “plaque-forming units” (“PFU”). The term “colony-forming unit” (“CFU”) is an estimate of viable bacterial numbers. The appearance of a visible colony requires significant growth of the initial cells plated—at the time of counting the colonies it is not possible to determine if the colony arose from one cell or 1,000 cells. Therefore, the results are given as CFU/mL (colony-forming units per milliliter) for liquids, and CFU/g (colony-forming units per gram) for solids to reflect this uncertainty (rather than cells/mL or cells/g).

As used herein, the “lytic” cycle means bacteriophage replication results in the destruction of the infected cell and its membrane. In the lytic cycle, the viral DNA exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA. In contrast, the “lysogenic” cycle used herein is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circular replicon in the bacterium's cytoplasm. In this condition the bacterium continues to live and reproduce normally. The genetic material of the bacteriophage, herein called a “prophage”, can be transmitted to daughter cells at each subsequent cell division, and a later event (such as nutrition depletion, UV radiation or the presence of certain chemicals) can release it, causing proliferation of new phages via the lytic cycle. As used herein, the “multiplicity of infection” (“MOI”) is the ratio of infectious agents (e.g. phage or virus) to infection targets (e.g. cell or bacteria). For example, when referring to a group of bacterial cells inoculated with infectious phage particles, the multiplicity of infection or MOI is the ratio of the number of infectious virus particles to the number of target cells present in a defined space.

Cf bacteriophage has binding specificity for citrus canker bacterium Xanthomonas citri subsp. citri, and is capable of lysing infected host Xanthomonas cells. Cf phage can also grow through lysogenic cycle by integrating phage DNA into host genome. Particularly preferred Cf bacteriophages have biological activity (e.g., the ability to lyse host cells and/or the ability to produce phage progeny in a host cell). The invention further contemplates “variants” or “strains” of Cf phages, which are phages having variation(s) less than 10% differences in the genomic sequences and polypeptides encoded thereby while retaining the same or different general genotypic and phenotypic characteristics as the parental Cf phage. Variants of Cf phages encompass polymorphic variants, such as XacF1 phage, which difference of nucleotide sequence from Cf (Cf1c or Cf1t) is less than 1% (Kuo, et al., 1991; Ahmad, et al., 2014). The invention also contemplates “recombinant” Cf phages, which are Cf phages having modified genotypic or phenotypic characteristics relative to the deposited Cf bacteriophage, particularly encompass specifically designed Cf bacteriophage harboring genes encoding novel phenotypic traits. Such recombinant Cf phages are engineered to contain or lose genes having traits not found in wild-type Cf phage. If not specified, “Cf variants” in this invention include (1) “Cf1t, Cf1c, Cf1tv, Cf16, Cf16-v1, Cf-tv2”, (2) “Cf mutants induced by chemical mutagens”, and (3) the recombinant Cf bacteriophages”. “Recombinant bacteriophages” or “recombinant phages” will mean genomic materials (nucleotides, DNA, RNA, proteins) of phages are artificially engineered and have the same nucleotide and amino acid sequences where one or more residues are added, deleted, or substituted. Cf2 and its “variants” in this invention will include “Cf2 mutants” induced by chemical mutagens and “the recombinant Cf2 phages”. If not specified, “Cf-type phages” in this invention include “Cf, XacF1, and Cf2 phages” because they are all able to infect Xanthomonas citri. Xf or Xp12 “variants” in this invention will include “Xf or Xp12 mutants” induced by chemical mutagens and “the recombinant Xf or Xp12 phages”.

As used herein, “immune” or “immuned” will mean that bacteria that have been infected by a phage and they are not susceptible for infection by the other phage. “Superinfect” or “Superinfection” will mean a phage is still capable of infecting an immuned bacteria.

EXAMPLES Example 1: Growth and Purification of Xanthomonas Citri Bacterium and Cf-Type Phages

Propagation of bacteria and phages is performed as described as the following, which are each hereby incorporated by reference in their entireties (Yang and Kuo, 1984; Kuo, 1987). Citrus canker pathogen, Xanthomonas citri subsp. citri (ATCC 49118), isolated from the lime Citrus aurantifolia in Florida was purchased from ATCC (Manassas, Va.). Unless specified, it is used as a bacterial host for cultivation of Cf-type phages and variants such as Cf1t, Cf1c, Cf1tv, Cf16, Cf16-v1, Cf-tv2, XacF1, Cf2, and the recombinant Cf and Cf2 phages. Xanthomonas citri subsp. citri was grown in potato-sucrose medium (PS medium), which contained, per liter: fresh potato, 200 g; Ca(NO₃)₂, 0.5 g; Na₂HPO₄.12H₂O, 0.2 g; peptone, 5 g; sucrose, 15 g. Alternatively, the Luria Broth (LB) medium is used (10 g tryptone, 5 g yeast extract, and 10 g NaCl per liter). The bacterial cells are plated or streaked on LB agar plates and grown at 30° C. for 48 hr. These plates are then stored at 4° C. Phages are harvested from semi-confluent lysis on double-layer LB plates. Distilled water or buffer is added to the plates, which are kept overnight in a cold room. The phage solution is collected and the cell debris is removed by centrifugation at 10000 g-force for 30 min at 4° C. The phage titer is assayed by the double-layer agar method. The phage is stored at 4° C. for use.

Cf-type phages are purified as described in (Kuo et al., 1987), which is hereby incorporated by reference in its entirety. An overnight infected Xanthomonas citri subsp. citri bacterial culture is harvested, and host cells and debris is removed by centrifugation at 6000 g-force for 10 min. Solid NaCl is added to the supernatant to a final concentration of 0.05 M, and polyethyene glycol 6000 is then added to a final concentration of 3%. After thorough stirring, the mixture is allowed to settle overnight in a cold room. The precipitate is collected by centrifugation at 6000 g-force for 10 minutes and then resuspended in distilled H₂O. Further purification was carried out by centrifugation through a CsCl step density gradient, (1.18, 1.25, 1.29, 1.34, and 1.39 g/ml) in a Beckman SW41 swinging bucket rotor at 23,000 rpm for 22 hr at 5° C.

The comparison of the lytic effect during Cf (left) and Cf1t (right) infection on the plague morphology of Xanthomonas citri on the agarose PS culture plate is shown in FIG. 1A. Cf1t phage DNA can integrate into Xanthomonas citri genome and becomes lysogenic, therefore it does not generate plagues as Cf. FIG. 1B shows long filament-like morphology of purified Cf1t phage stained with 2% phosphotungstic acid under electronic microscopy (Kuo et al., 1987).

Example 2: Purification of Replication Form (RF) and Phage DNA of Cf-Type Phages and Xanthomonas Citri Genome DNA

Preparation of the RF DNAs of Cf-type phages and their variants such as Cf1t, Cf1c, Cf1tv, Cf16, Cf16-v1, Cf-tv2, XacF1, Cf2, Cf2 mutants and the recombinant Cf-type phages from host bacteria are performed as described (Yang and Kuo, 1984), which are each hereby incorporated by reference in their entireties. Xanthomonas citri subsp. citri is grown in 500 ml PS or LB medium at 28° C. The cells, at a density of 2×10⁹ per ml, are infected with Cf-type phages at a multiplicity of 20 and treated with 170 ˜mg/ml chloramphenicol at 10 min post-infection. Chloramphenicol is added to increase the synthesis of RF DNA and to prevent chromosomal DNA synthesis. After 4 hours of incubation at 28° C., the infected bacterial cells are harvested, chilled, washed once with 250 ml buffer (10 mM-Tris-HCl pH 8.0, 0.1 mM-EDTA) and lysed with SDS and NaOH. After lysis, the lysate is centrifuged at 44000 g-force for 90 min, and 1/30 volume of 3 M-sodium acetate and 0.6 volume isopropanol are added to the supernatant. After centrifugation at 27200 g-force for 20 min, the pellet is resuspended in 5 ml Tris-glucose (25 mM-Tris-HCl, pH 8.0, 10 mM-EDTA, 50 mM glucose) and 15 ml 5 M-potassium acetate. The bacterial DNA and debris are spun down at 27200 g-force for 20 min. The supernatant, containing the RF DNA, is precipitated with 2 volume ethanol at −20° C. for 2 to 4 hours and recovered by centrifugation at 12000 g-force for 30 min. The pellet is dissolved in 8 ml TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The DNA is then purified by centrifugation to equilibrium in a CsCl-ethidium bromide density gradient. Each Quick-Seal polyallomer centrifuge tube contained 5 ml of sample, 1.5 mg ethidium bromide and 5.05 g CsCl. Centrifugation is performed at 479000 g-force at 15 to 20° C. for 3.5 to 4 hours using a NVT-100 Beckman rotor. At the end of the run, the band containing supercoiled DNA is collected by inserting a hypodermic needle into the side of the tube. Ethidium bromide is removed by five extractions with water-saturated n-butanol. The samples are mixed with 2 volumes of distilled water and precipitated with 2.5 volumes of 100% ethanol. The DNA thus prepared is used directly for restriction endonuclease digestion or PCR. Digestion of RF DNA with restriction endonucleases, and gel electrophoresis and purification of restriction DNA fragments are performed as described in (Yang and Kuo, 1984), which is hereby incorporated by reference in its entirety.

DNAs from Cf-type phages and infected Xanthomonas citri subsp. citri are purified as described in (Kuo et al., 1987), which is herein incorporated by reference in its entirety. A purified phage suspension is dialyzed against TEN (25 mM Tris-HCl; 10 mM EDTA and 0.15 M NaCl, pH 8.5). The phage protein coat is then dissociated by adding sodium dodecyl sulfate (SDS) to a final concentration of 2%. The proteins are further digested with Pronase (1 mg/ml) at 60° C. for 18 hr or overnight. Contaminating RNA is digested by the addition of RNase A (50 z,21 g/ml) and incubated at 37° C. for 1 hr. NaClO₄, is added to a final concentration of 1 M and an equal volume of PIC (TEN-saturated mixture of phenol:isoamyl alcohol:chloroform (25:1:24) was then added. This mixture is shaken thoroughly for 15 min. After 5 min centrifugation at 9000 g-force, the aqueous phase is collected and the phage DNA is precipitated with ethanol. The pelleted phage DNA is dissolved in TEN and dialyzed against two changes of TEN with 2 M NaCl, and then finally against TEN. To isolate DNA from X. citri cells, logarithmically growing bacterial cells at 2 to 4×10⁹ cells/ml are harvested by centrifugation, washed with 5 ml of 100 mM Tris-HCl, 10 mM NaCl at pH 7.6, and suspended in 1.8 ml of 50 mM Tris-HCl (pH 7.6) 100 mM NaCl, and 5 mM disodium EDTA. The washed cell suspension is lysed by the addition of lysozyme solution (10 mg/ml in H₂O 10 min at room temperature) and 0.2 ml of 20% SDS to the buffered cell suspension. The lysed cell suspension is extracted with phenol: chloroform: isoamyl alcohol (24:24: 1) until no interface could be detected between the aqueous and organic phases. The aqueous phase is precipitated with 2 volume of −80° C. ethanol. The ethanol precipitate is collected by centrifugation at 13,000 g-force for 10 min, air dried, and suspended in 2 ml of 50 mM Tris-HCl (pH 7.6) 100 mM NaCl, and 5 mM EDTA. This solution is incubated with 200 units of RNase A (New England BioLabs, Ipswich, Mass.) at room temperature for 4 hours. The RNase-treated solution is extracted three times with phenol:chloroform:isoamyl alcohol. The aqueous phase is precipitated twice with ethanol, and the dried precipitate is suspended in 10 mM Tris-HCl (pH 7.6) and 0.1 mM disodium EDTA. Digestion of Cf-type phage or host bacterial DNA with restriction endonucleases, agarose gel electrophoresis, transferring DNA to a nylon membrane and hybridization, DNA sequencing are performed in (Kuo et al., 1987; Dai, et al., 1988), which are hereby incorporated by reference in their entireties.

The example of Cf phage DNA integration into Xanthomonas citri genome is shown in FIG. 2. The Cf16-v1 attachment site is localized to the unique PstI-KpnI fragment by restriction mapping (FIG. 2A). HindIII cleaves the circular Cf16-v1 RF into two fragments of approximately 5.8 and 1.8 kb, respectively. Three lysogen HindIII fragments with a size of 1.8, 3.0 (H′), and 4.3 (H) kb, respectively, hybridize to the Cf16 probe (Dai et al., 1987). FIG. 2B shows the nucleotide sequence of Cfl6-v1 in the vicinity of the phage attachment site. The common core sequence, inverted repeats, potential recognition sequences for a site-specific recombination enzyme, repeated sequences, potential binding site of another protein factor, are identified. Based on the nucleotide sequence alignment, Cfl6-v1 genome is integrated within the X. citri host gene called (3R)-3-hydroxyacyl-[acyl-carrier-protein]:NADP+oxidoreductase (FIG. 2C)(Dai et al., 1988). The physical map of Cf RF DNA, including the location of phage genes and cleavage sites of the restriction endonucleases, is shown in FIG. 3A. Except for ORF 165, transcription of all the investigated genes proceeds clockwise. (Cheng et al., 1999)

Example 3: Quality Control Assays for Cf-Type Phage Infection

Quality control assays for immunity, phage infectivity, phage yield, and viable colonies after Cf-type phage infection are performed as described in (Kuo et al., 1987), which are hereby incorporated by reference in their entireties. Samples taken from the culture are spread onto LB agar plates. After colony formation, a single colony is chosen and transferred to LB broth for 24 hours at 30° C. For assay of immunity a sample from this culture is mixed with broth soft agar and poured onto an LB plate. Cf phage suspension (0.01 ml) is spotted onto the layer containing bacteria to be tested. Sensitive cells formed a clear zone and immune cells did not. For determination of phage infectivity and phage yield the sample from the above culture is centrifuged at 10,000 g-force for 20 min to remove cell debris. The 0.01 ml samples from dilutions of the supernatant are plated with sensitive bacteria. The viable colony count is made by spreading the cells on LB plates and incubation at 28° C. for 3 days.

The growth curve for bacteria after Cf-type phage infection is determined as the following (Kuo et al., 1987) which is herein incorporated by reference in its entirety. Infected bacteria are suspended in LB at a concentration of 1×10⁸ cells/ml and incubated at 30° C., with shaking. At different intervals, samples are diluted and spread on LB agar plates. After colony formation the number of colonies is counted.

The methods of preparation of Cf-type phage infection culture and microculture technique are performed as the following (Kuo et al., 1994), which is herein incorporated by reference in its entirety. TSG liquid medium contains 5 g NaCl, 5 g bacto-soytone, 10 g bacto-tryptone and 2 g glucose per liter. To produce solid media for colony formation assay or for microculture, 1.5% or 0.75% agar respectively are added. Kanamycin is used at 100 mg/ml. A single colony of host bacteria is transferred into 5 ml TSG liquid medium and grown at 28° C. with shaking. After reaching its log phase, the concentration of bacteria is about 5×10⁸ cfu/ml, and the phage at MOI of 10 are added. The infected cultures are grown for the time required for each experiment. Bacteria at a concentration of 5×10⁸ cfu/ml are infected with Cf-type phages or their variants at MOI of 10. At different time intervals, samples are taken and spread on TSG agar plates previously poured on concave slides. The slides are placed in petri dishes and incubated at 28° C. for 16 hours. Extent of cell division is examined with a light microscope. At this stage the uninfected cells have already divided into about 32 cells. The respective cell types are determined and calculated as percent of total population.

Assays for surviving host Xanthomonas citri cells, Cf-type phage-resistant, Cf-type phage-releasing and Cf-type phage-containing cells, are performed as described with modification (Kuo et al., 1994), which is herein incorporated by reference in its entirety. Host bacteria are infected with phage, and samples are spread on TSG agar plates. The number and size of colonies formed is determined directly and used to calculate the respective percentage. In order to determine the cell types of these colonies they are transferred onto two different agar plates by replica plating. One plate is seeded with Cf-type phage or their variants (10⁹ pfu per plate) for detection of phage-resistant cells. The other plate is seeded with sensitive bacteria to detect lysis by phage-releasing cells. The lysogen should grow to unchanged colonies on the first plate, and release phage and form plaques on the second plate.

An example is shown that cell division of Cfltv-infected Xanthomonas citri cells was monitored using a microculture technique (FIG. 4). Bacterial cells were observed by light microscope after 16 hour incubation at 28° C. The normal cells divided and grew into separate colonies. Cfltv-infected cells were still undivided. (Kuo et al., 1994)

Example 4. Electroporation of Cf Phage DNA into Xanthomonas Citri Bacteria, RNA Extraction, and Primer Extension

Cf-type phages and their variant DNAs are either purified by isolating phage particles as described in Example 2, or are directly synthesized by a company (GenScript, Coralville, Iowa). The synthesized DNA fragments are ligated and subcloned into a kanamycin-resistant pUC57 vector and amplified in E. coli. An example is shown that the synthesized 7.3 kb Cf1-tv2 DNA fragments are subcloned into pUC57 vector, digested with restriction enzymes and analyzed in 1% agarose gel. (FIG. 16).

The electroporation method to transform phage or RF DNAs of Cf-type phages and their variants into Xanthomonas citri subsp. citri cells is performed as the following (Yang et al., 1991), which is herein incorporated by reference in its entirety. Bacterial cells are grown for 16 hour and chilled, sedimented and resuspended in 0.5 volume of the buffer (200 mM Tris-HCl; 1 mM EDTA and 1 M NaCl, pH 7.5). After even mixing and centrifugation, bacterial pellets are washed and resuspended at TMN buffer (50 mM Tris-HCl; 50 mM MgSO₄ and 80 mM NaCl, pH 7.5) on ice for 2 hours. Pellets from centrifugation separation are then washed and resuspended in deionized water to remove ion. 1 to 2 micro g RF DNA of Cf-type phages in 5 ml deionized water was added to 40 ml bacterial suspension. After even mixing, the mixture was poured into a precooled cuvette (VWR, Radnor, Pa.) and subjected to appropriate pulse at 12.5 kV/cm, 25 ml micro F, 400 Ω for 7 to 9.3 mini-seconds.

RNA isolation and Northern hybridization is performed as described previously (Cheng et al., 1999), which is herein incorporated by reference in its entirety. Primer extension experiments are carried out using the method described by (Cheng et al., 1999). Synthetic oligonucleotides for cM1(5′-CAGGATCGAATATGGATGCACGGTGTA-3′) and cM2 (50-TGACAGAGAGGACAGTGAAAACTATAC-30) complementary to the sequence position 5701-5728 and 5475-5502 (FIG. 5), respectively, are used for both primer extension reaction and DNA sequencing.

Electroporation of X. citri cells yields frequency as high as 5.2×10⁹ pfu per microgram of DNA. Both RF DNA and the single-stranded phage DNA were efficiently accepted by X. citri cells in the same condition (Yang et al., 1991).

Mutation sites on the cf-tv2 and Cf1tv (also called cf-tv1) mutation on the Cf genome are shown in FIG. 3B. The 49 base pair deletion of cf-tv2 is upstream of ORF 165, which contains the attachment site (attP) for integration in the phage. The Tin the start codon of ORF165 is mutated of the single base substitution in Cfltv. Using primer extension to detect the transcription start sites, there are two transcripts, cM1 and cM2, generated from ORF165 region at opposite directions. The 5′ end of the cM1 transcript is located at G5629, while the 5′ end of the cM2 transcript is at C5693 (FIG. 5A). There are −35 and −10 consensus sequences of a predicted promoter region identified in the upstream sequence of ORF165 (Cheng et al., 1999).

Example 5. Generation and Application of Cf-Type Phages that can Inhibit X. Citri Growth and Suppress Citrus Canker Disease

Analysis of DNA sequence and organization reveals the superinfection activity of Cf1tv and Cf-tv2 is mapped at the upstream sequence of ORF165 that contains a predicted promoter region encoding cM1 and cM2 transcripts (FIG. 3, FIG. 5B, FIG. 15) (Cheng et al., 1999). Cf-tv2 has 49 base-pair deletion at upstream of ORF 165, whereas Cfltv has T to A substitution in the start codon of ORF165. This T is also located next to −10 consensus TATA box of a predicted promoter for cM1 transcript (FIG. 5B). In addition, the virulent Cf variant XacF1 also contains G to A substitution at this −10 TATA box (FIG. 15). These results demonstrate that this predicted promoter is the determinant for phage immunity.

Cf2 and Cf phage shares almost no sequence homology in their entire genome except the starting 58 nucleotides of cM2 transcript of Cf is 95% identical to Cf2. The −35 and −10 consensus sequences are also found in the upstream of ORF162 in Cf2 (FIG. 15), indicating that the critical domain for phage immunity is also conserved in Cf2. These findings suggest that Cf2 can be also engineered into a virulent variant as a bio-control reagent against citrus canker pathogen.

This invention claims the applications of Cf-type phages, such as Cf, Cf1c, Cf-tv1, Cf-tv2, XacF1, Cf2 and their mutants “Cf-M” to inhibit X. citri growth in an orange grove.

(1) “Cf-M” phage is generated by serial passages or artificially induced mutations within the sequence of Cf-type phage genomes (SEQ ID NO:1, 24, 25), where one or more nucleotides are added, deleted, or substituted. Artificially induced mutations are conducted by treating Cf, Cf1c, Cf-tv1, Cf-tv2, XacF1, Cf2 phages with mutagens such as, but not limited to, ethyl methanesulfonate and sodium nitrite, as described (Sega, 1984; U.S. Pat. N. 3,052,606 A; September 1962), (FIG. 6A), which are herein incorporated by reference in their entireties.

(2) Cf, Cf1c, Cf-tv1, Cf-tv2, XacF1, Cf2 and Cf-M phages are propagated and purified as Example 1 and 2. Phage infectivity assay is performed as the following. One milliliter of X. citri culture is centrifuged, and the supernatant is filtered through a 0.45-micro meter-pore-size filter to remove any residual bacteria. The filtrate is serially diluted in LB medium, and 10 ml of each dilution is mixed with 100 ml of mid-log-phase culture of X. citri and 3 ml of soft agar (0.75%) in LB broth. The mixture is poured and spread evenly onto an agar plate. The plate is scored for plaque formation after incubation at 28° C. for 18 hours. Quality controls of these different Cf-type or Cf-M phages are assayed as Example 3, and the individual clones that yield the highest inhibitory efficiency on the bacterial growth will be selected for further application in the field. Phage particles are aliquoted (herein called “phage stock”) and stored in distill water or a proper buffer at 4° C.

(3) Field tests of susceptible citrus varieties with these Cf-type or Cf-M phages are performed to compare the disease severity caused by the citrus bacterial canker in one-quartre acre (0.1 ha) for each treatment. A phage stock is diluted into water or a solution in a proper ratio, and sprayed or misted to coat on the citrus trees and/or fruits once a week for 5 times. After the phage treatment, the leaf and fruit bacterial canker infested rates of different citrus varieties are investigated. Different Cf and variants phages are screened for the control of X. citri subsp. citri with better pathogen inhibition effect than others. Cf-type or Cf-M phages with the greatest inhibitory effects on citrus canker in field tests are selected for the large-scale production and commercial use. The detailed process flowchart is further described in FIG. 6C.

(4) This application also claims an application of using a recombinant Cf-type phages (herein called “Cf-Super” phages), which can superinfect and kill “immuned” X. citri bacteria, to treat citrus canker disease. To generate Cf-Super phages, a series of mutations are generated to mutate nearby or within the sequence of ORF165 to change the determinant domain of phage immunity (SEQ ID NO:1, 2, 24, 25), where one or more nucleotides are added, deleted, or substituted, in RF DNAs of Cf-type phages and their variants (FIG. 6B, 15). These recombinant RF DNAs will be electroporated into X. citri cells as Example 4. Cf-Super phages are propagated in cells and released into the LB medium. Cf-Super phage particles are harvested and purified from LB medium as Example 1. Phage infectivity assay, quality control, and application in the field are performed as described as (2) and (3). Cf-Super phages with the greatest inhibitory effects on citrus canker symptoms in field tests will be selected for the commercial use. Cf-Super phages cause the lysis of X. citri, and new phages are released to infect more bacteria in a lesion of citrus canker. The detailed process is described in FIG. 6C.

Example 6. Generation and Application of a Controllable “SS-iCf” Phage that Only Infect and Kill X. Citri Bacteria Once but will Not Spread and Replicate After Used

This invention claims the applications of a method that generates recombinant “SS-iCf” phages which infectivity is controllable by performing the following steps (FIG. 7):

(1) Escherichia coli or X. citri bacteria mutants (herein called “bacteria mutants”) that are insufficient to grow in a selected nutrition medium (e.g., a medium lack of specific amino acids or essential components) is prepared by removing essential nutrition genes via the site-directed gene replacement mutagenesis (Oshiro et al, 2006).

(2) “Component A”: A plasmid containing DNA fragments encoding Cf-type phage coat protein A, a protein having the amino acid sequence of SEQ ID NO: 5, 32, 44, or proteins having the same amino acid sequences where one or more amino acids are added, deleted, or substituted amino acids, is cloned in a broad-host-range expression DNA vector (e.g., pUC8, pRK415, pRKD418 etc.) (Mather et al., 1995). This DNA vector also contains an essential nutrition gene X that can compensate nutrition deficiency of bacteria mutants as described in (1). These DNAs (herein called “component A”) are electroporated into Escherichia coli or X. citri bacteria mutants as Example 4, grown in a selected nutrition medium, and purified as Example 2.

(3) “Component B”: A DNA fragment of an essential nutrition gene Y (different gene from component A) is amplified by polymerase chain reaction (PCR), and subcloned into RF DNA of Cf-type phages to replace the coat protein A gene of Cf-type phages, variants, or Cf-Super phages. These recombinant RF DNAs containing a nutrition gene Y (called “component B”) are electroporated into X. citri cells bacteria mutants and grown in a selected nutrition medium. Component B is then purified as Cf RF DNA in Example 2. Due to the loss of the essential coat protein A gene, component B alone cannot produce infectious phage particles.

(4) To generate a controllable, “single-shot infectious” Cf-type (herein called “SS-iCf”) phage, Component A and B will be electroporated together into X. citri mutants lack of nutrition genes X and Y, then bacteria are grown in a selected nutrition medium at 28° C. SS-iCf phage particles are harvested and purified from growth medium as Example 1. The detailed strategy is further illustrated in FIG. 7. Phage infectivity assay is performed as Example 5. The individual clones that yield the highest inhibitory efficiency on the bacterial growth but do not infect bacteria for the second time will be selected for further application in the field. Phage stocks are aliquoted and stored in distilled water or a proper buffer at 4° C. Field tests are performed as Example 5, and the greatest inhibitory phage clones will be selected for further application of commercial use. SS-iCf phages can infect and kill X. citri cells by the lysis of bacterial cells. Because the genome of SS-iCf phages do not contain the coat protein A gene, it cannot propagate in the filed anymore and can only be used for one time.

Example 7: Methods to Improve the Storage Shelf Life of Cf-Type Phages

This invention claims a method to apply and engineer a recombinant Cf-type phage to increase its shelf life for storage purpose. These recombinant Cf-type phages are packed with the major coat protein B from other filamentous Inoviridae phages which has more stable biochemical properties (herein called “Cf-XC phages”) as the following steps (FIG. 8):

(1) The DNA fragments (herein called “XC DNA fragments”) are nucleotides encoding a protein (coat protein B) having the amino acid sequence of SEQ ID NO: 13 to 22 (such as, but not limited to, an example of SEQ ID NO: 23 from phiLf phage), or proteins having the same amino acid sequences where one or more amino acids are added, deleted, or substituted amino acids.

(2) These XC DNA fragments are amplified with PCR and cloned into RF DNAs of Cf-type phages, their variants, Cf-M, Cf-Super, and SS-iCf phages to replace the major coat protein B gene of Cf-type phages. These RF DNAs containing XC fragments are electroporated into X. citri bacteria, amplified and purified as Cf RF DNA as Example 2. The Cf-XC phage particles from the growth medium are also harvested and purified as Example 1. The detailed strategy is further illustrated in FIG. 8A. Phage infectivity assay and the application of Cf-XC phage particles in the field tests are the same as Example 5, and the greatest inhibitory phage clones will be selected for further application. Cf-XC phages cause the lysis of X. citri, and new Cf-XC phages are released to infect more bacteria in a lesion of citrus canker.

To generate a controllable, “single-shot” infectious Cf-XC phages (herein called “SS-iCf-XC phages”), the procedure is performed as following (FIG. 8B):

(3) Component C: XC DNA fragments are cloned in a broad-host-range expression DNA vector that also contains an essential nutrition gene X. These plasmid DNAs (herein called “component C”) are transformed into Escherichia coli or X. citri bacteria mutants, grown in a selected nutrition medium, and purified.

(4a) Component D: A DNA fragment of a nutrition gene Y is amplified by PCR and subcloned into RF DNA to replace the major coat protein B gene of Cf-type phages and their variants, Cf-Super, and SS-iCf phages. These recombinant RF DNAs (herein called “component D”) will be electroporated into X. citri bacteria mutants as described in Example 4. Cells are able to grown on a selected nutrition medium, and component D is purified as Cf RF DNA as described in Example 2.

(4b) Component E: A site-specific insertion with two nucleotides is introduced into the nucleotide position corresponded to the first codon in the ORF of major coat protein B in RF DNAs of Cf-type phage and their variants (e.g., between nucleotide 313 and 314 of SEQ ID NO: 1; nucleotide 3817 and 3818 of SEQ ID NO: 25) using PCR. This insertion causes Cf-type RF DNAs unable to encode major coat protein B. These recombinant RF DNAs (herein called “component E”) are electroporated into X. citri cells as described in Example 4, and component E is purified as Cf RF DNA as described in Example 2. Due to the loss of the major coat protein B gene, component D or E alone cannot produce any phage particles.

(5) The mixture of “Component C and D”, or “component C and E”, is electroporated into X. citri bacteria mutants lack of nutrition genes X and Y, respectively, then cells are grown in a selected nutrition medium at 28° C. SS-iCf-XC phage particles are harvested from the medium as described in Example 1. The detailed strategy is further illustrated in FIG. 8B. Phage infectivity assay and the application of SS-iCf-XC phage particles in the field tests are the same as Example 6. Because the genome of SS-iCf-XC phages do not contain the coat protein B gene, these recombinant phages cannot produce new phage particles in the filed anymore and can only be used for one time.

An alternative way to generate SS-iCf-XC phages is also claimed in this patent. Component B in Example 6 is used instead of Cf-type RF DNAs for cloning in step (2), (4a) and (4b) to generate “component F”, “component G”, and “component H”, respectively. Component F, G, or H cannot generate phage particles because they do not have coat protein gene A and B. The DNA mixtures of “Component A+F”; “component A+C+G” and “component A+C+H” will be electroporated into X. citri bacteria mutants lack of nutrition genes X and Y. Cells are grown in a selected nutrition medium at 28° C. SS-iCf-XC phage particles will be harvested from growth medium. Phage infectivity assay and the selection and application of SS-iCf-XC phage particles in the field tests for commercial use are the same as Example 6.

Example 8: Generation and Application of “Cf-Killer” Phages to Carry Genes Causing the Lysis of Bacterial Cells

This invention claims a method to generate a recombinant Cf-type phage (here called “Cf-killer phage”) that contains toxic genes to kill or inhibit X. citri bacteria growth. Gene materials (such as DNA fragments) that encode nucleic acids or amino acid products (such as, but not limited to, lysozyme from chicken egg white) able to interfere with bacterial growth or lead to bacterial cell lysis are cloned into RF DNAs of Cf-type phages, their variants, and recombinant Cf-type phages described in Example 5, 6 and 7. These recombinant RF DNAs (herein called “component I”) will be electroporated into X. citri cells as described in Example 4, Cf-killer phage particles are harvested from growth medium as described in Example 1. The detailed strategy is further illustrated in FIG. 9A. Phage infectivity assay and the application of Cf-killer phage particles in the field are the same as Example 5. Cf-killer phages cause the lysis of X. citri, and new Cf-XC phages are released to infect more bacteria in a lesion of citrus canker.

To generate a controllable or “single shot” infectious Cf-killer phage (herein called “SS-iCf-killer phage”), the DNA fragments, which encode nucleic or amino acid products to interfere with bacterial growth or lead to bacterial cell lysis, are cloned into component B (herein called “component J”). Due to the loss of the essential coat protein A gene, component J alone cannot produce infectious phage particles. The DNA mixture of component A and I will be electroporated together into X. citri bacteria mutants, then cells are grown in a selected nutrition medium at 28° C. SS-iCf-killer phage particles are harvested from growth medium as described in Example 1. Phage infectivity assay and the application of SS-iCf-killer phage particles in the field are the same as Example 6. Because the genome of SS-iCf-killer phages do not contain the coat protein A gene, these phages cannot produce new infectious phages in the filed anymore and can only be used for one time. The detailed strategy is further illustrated in FIG. 9B.

Example 9. Generation and Application of “Cf-Shuttle” Phage as a Vector to Carry Foreign Genes that Integrate into X. Citri Genome

This invention claims that a method to generate a vector (herein called “Cf-Shuttle”) to deliver foreign genes that can integrate into X. citri genome (FIG. 10). The DNA fragments, which encode nucleic acid or amino acid products are cloned to replace coat A gene in RF DNA of Cf-type phages (herein called “Component K”). The mixture of Component K and component A are electroporated together into X. citri mutants as described in Example 4. Cells are grown in a selected nutrition medium at 28° C. Cf-shuttle vector phage particles are harvested from growth medium as described in Example 1. The rate of integration of Cf shuttle vector into X. citri genome is assayed as Example 2 and 4. The detailed strategy is illustrated in FIG. 10.

Example 10. Purification, Engineering and Application of Xp12 Phage to Inhibit Rice Blight Disease in the Field

This application claims methods to generate Xp12 phage as a bio-control tool that inhibit rice blight disease in the field. Xp12 phage (ATCC 27931-B1) and its host Xanthomonas oryzae are purchased from ATCC. Bacteria are routinely grown at 28° C. in TSG medium as described in Example 1. Phage infection is normally performed by adding CsCl-purified phages to the bacterial culture in early exponential phase (an OD600 value of 0.3-0.4) at a MOI of about 10.

(1) Phage genome DNA is isolated and purified from CsCl-purified Xp12 phage by phenol-chloroform extraction and precipitation with 100% ethanol. Purified DNA is digested with restriction enzymes KpnI, DpnI, EcoRV, and NdeI, and cloned into pBlueScript II vector (Agilent Technologies) for DNA sequencing. Mutations of phage DNA where one or more nucleotides or genes are added, deleted, or substituted are cloned using PCR or generated by treatment with ethyl methanesulfonate or sodium nitrite. These chemical-mutated or recombinant Xp12 phage DNAs (called “Xp12 variants”) are electroporated into X. oryzae bacteria, and Xp12 variant phage particles are harvested and purified from growth medium as Example 1. Phage infectivity assay are performed as Example 5. The individual clones that yield the highest inhibitory efficiency on the bacterial growth will be selected for the field test as described below.

(2) Phage stocks are aliquoted and stored in 10 mM Tris, 50 mM CaCl₂, pH 8.0 (Tris-CaCl₂ buffer) at room temperature or 4° C. In a rice field, a phage stock is diluted in Tris-CaCl₂ buffer, and field tests are performed as the following:

-   -   (a) Detached leaf assay: To determine the virulence and relative         aggressiveness, the suspensions of different isolates of         Xanthomans oryzae from ATCC obtained from the different rice         zones were applied on leaves of eight rice varieties. The         detached leaves were placed on 3-folded blotting paper towel in         petri plates and inoculated with bacterial suspension containing         10⁸ cfu/ml through pin prick method. The inoculated leaves were         incubated at 22° C., the lesion length measured in cm and data         analyzed statistically by ANOVA and significance at 5% level was         tested by Duncan's multiple range test (DMRT).     -   (b) Glass house assay: In glass house experiment seeds of         various rice varieties were grown on moist sterilized filter         paper in Petri plates, maintained in a growth chamber at         30-35° C. Two weeks old seedlings were transplanted to small         plastic pots (diameter 13 cm) and placed in glass house at         pre-tillering stage. The plants were again transplanted to         bigger plastic pots (diameter 27 cm) and three leaves per         isolate were inoculated using clipping method. The control was         treated simply with sterilized Tris-CaCl₂ buffer. The lesion         size was measured after 12-14 days.     -   (c) Field assay: Field trials for testing         pathogenicity/virulence of different isolates of X. oryzae were         conducted at fields. For nursery raising the seeds of rice         variety were soaked (100 g/m²) overnight and sown during the         first week of June. The seeds were spread on seed bed covered         with dried plant material (wheat or rice straw) and kept moist         by adding water. After one month (in the first week of July) the         seedlings were removed from the nursery and transplanted in the         field.     -   (d) Inoculation/treatment: Sixty to seventy days old rice plants         were inoculated with Xp12 phages or recombinant variants,         together with various isolates of X. oryzae, using clipping         method of inoculation. The lesion size was measured after 12-14         days.

Xp12 phages and variants with the greatest inhibitory effects on X. oryzae growth are selected based on the field test results for the further application and commercial use. Xp12 variant phages cause the lysis of X. oryzae, and new Xp12 variant phages are released to infect more bacteria in the rice field. The detailed strategy and process flowchart is further illustrated in FIG. 11A.

Example 11. Generation and Application of a Controllable “SS-iXp12” Phage that Only Infect and Kill X. Oryzae Bacteria Once but will Not Spread and Replicate After Use

To generate the controllable, “single-shot infectious” Xp12 phage (herein called “SS-iXp12” phage), the procedures are described as the following (FIG. 11B):

(1) Escherichia coli or X. oryzae bacteria mutants that are insufficient to grow in a selected nutrition medium (e.g., a medium lack of specific amino acids or essential components) is prepared by removing essential nutrition genes via the site-directed gene replacement mutagenesis.

(2) “Component L”: A plasmid containing DNA fragments encoding coat protein and/or RNA polymerase genes of Xp12 phage, or proteins having the same amino acid sequences where one or more amino acids are added, deleted, or substituted amino acids, was cloned in a broad-host-range expression DNA vector. This DNA vector contains an essential nutrition gene X that can compensate nutrition deficiency of bacteria mutants as described in (1). These DNAs (herein called “component L”) are electroporated into Escherichia coli or X. oryzae bacteria mutants as Example 4, grown in a selected nutrition medium, and DNAs are purified as Example 2.

(3) “Component M”: A DNA fragment of two essential nutrition genes Y and Z (different gene from component L) is amplified by polymerase chain reaction (PCR), and subcloned into Xp12 DNA to replace the coat protein and RNA polymerase gene of Xp12 phages or Xp12 variants in Example 10. These recombinant Xp12 DNAs containing nutrition genes (called “component M”) are electroporated into X. oryzae bacteria mutants and grown in a selected nutrition medium. Component M is then purified as described in Example 2.

Due to the loss of the essential coat protein and/or RNA polymerase genes, component M alone cannot produce phage particles and mediate infection. Component L and M are electroporated together into X. oryzae mutants lack of nutrition X, Y, and Z, then bacteria are grown in a selected nutrition medium at 28° C. SS-iXp12 phage particles are harvested and purified from growth medium as Example 1. Phage infectivity assay and quality controls are performed as Example 5. The individual clones that yield the highest inhibitory efficiency on the bacterial growth but do not infect bacteria for the second time will be selected for further application in the field as described as Xp12 variants. The field tests are performed as described in Example 10. SS-iXp12 phages with the greatest inhibitory effects on X. oryzae growth are selected based on the field test results for the further application and commercial use. Because the genome of SS-iXp12 phages do not contain the coat protein and RNA polymerase gene, it cannot propagate in the filed anymore and can only be used for one time. The detailed strategy and process flowchart is further illustrated in FIG. 11B.

Example 12. Purification, Engineering and Application of Xf Phage to Inhibit Rice Blight

This application claims methods to generate and apply recombinant or chemical-mutated Xf phages as a bio-control tool that inhibit rice blight disease in the field (FIG. 12).

Xf phage is propagated in Xanthomonas oryzae grown exponentially in PS or LB medium as described in Example 1. When the bacterial concentration reached 10⁹cells/ml, Xf phages are added to provide a final concentration of 10¹⁰ PFU per milliliter and continue to culture for 24 hours. At the end of cultivation the phage titer reaches 2.5×10¹² PFU/ml. Ten liters of crude lysate was used for phage purification. Host cells and debris are removed by centrifugation at 10,000 g-force for 20 min. Ammonium sulfate is slowly added to the supernatant, with stirring, to 30% saturation. The mixture is allowed to settle for 24 hours in a cold room. The precipitate is then collected by centrifugation and resuspended in one liter of 0.05 M phosphate buffer. For further clarification, the above procedures are repeated once. Finally the resulted precipitate is suspended in 20 ml of 0.05 M phosphate buffer, pH 7.0, and dialyzed against the same buffer to remove ammonium sulfate. Xf phage is then precipitated by centrifugation at 100,000 g-force for 3 hours. For further purification, the phage precipitates are suspended in CsCl at density of 1.260 and centrifuged to equilibrium in a SW-50 rotor at 146,821 g-force for 24 hours. The resulting dense band of Xf phage was collected and freed from CsCl by dilution with SSC (0.15 M NaCl, 0.015 M sodium citrate) and several cycles of washing by high speed centrifugation.

(1) RF DNA of Xf phage is purified as described in Example 2. Xf RF DNA is synthesized directly synthesized by a company (GenScript, Coralville, Iowa) based on the SEQ ID 26. The synthesized DNA fragments are ligated and subcloned into a kanamycin-resistant pUC57 vector and amplified in E. coli. Mutations of Xf phage DNA where one or more nucleotides or genes are added, deleted, or substituted are cloned using PCR or generated by treatment with ethyl methanesulfonate or sodium nitrite. These mutated or recombinant Xf DNAs (herein called “Xf variants”) are electroporated into Xanthomonas oryzae, and Xf variant particles are harvested and purified from growth medium as described above. Phage infectivity assay are performed as Example 5. The individual clones that yield the highest inhibitory efficiency on the bacterial growth will be selected for further application in the field. Phage stocks are aliquoted and stored in 0.1 M phosphate buffer, pH 7.0 at 4° C. The field tests of Xf variant phages are performed as described in Example 10. Xf variant phages cause the lysis of X. oryzae, and new Xf variant phages are released to infect more bacteria in the rice field. The detailed strategy and process flowchart is further illustrated in FIG. 12A.

(2) To generate a controllable, “single-shot infectious” Xf (herein called “SS-iXf”) phage, the following procedures are performed (FIG. 12B):

-   -   (a) “Component N”: A plasmid containing DNA fragments encoding a         protein having the amino acid sequence of SEQ ID NO: 13 and 57,         or proteins having the same amino acid sequences where one or         more amino acids are added, deleted, or substituted amino acids,         was cloned in a broad-host-range expression DNA vector. This DNA         vector contains an essential nutrition gene X that can         compensate nutrition deficiency of bacteria mutants. These DNAs         (herein called “component N”) are electroporated into         Escherichia coli or X. oryzae bacteria mutants, grown in a         selected nutrition medium, and DNAs are purified as Example 2.     -   (b) “Component O”: A DNA fragment of an essential nutrition gene         Y (different gene from component N) is amplified using PCR, and         subcloned into RF DNAs of Xf variants to replace their coat         protein B genes (e.g. nucleotide 4353-4583 in SEQ ID 26). These         recombinant Xf RF DNAs containing a nutrition gene Y (called         “component O”) are electroporated into X. oryzae cells bacteria         mutants and grown in a selected nutrition medium. Component O is         then purified as described in Example 2. Due to the loss of the         essential major coat protein B gene, component O alone cannot         produce Xf phage particles.     -   (c) Component N and O are electroporated together into X. oryzae         mutants lack of nutrition gene X and Y, then bacteria are grown         in a selected nutrition medium at 28° C. SS-iXf phage particles         are harvested and purified from growth medium as described         above. Phage infectivity assay and quality controls performed as         Example 5. The individual clones that yield the highest         inhibitory efficiency on the bacterial growth but do not infect         bacteria for the second time will be selected for field tests as         described in Example 10. Because the genome of SS-iXf phages do         not contain the major coat protein B gene, it can be only used         for one time and will not propagate in the filed anymore. The         detailed strategy and process flowchart is further illustrated         in FIG. 12B.         Ahmad A A, Askora A, Kawasaki T, Fujie M, Yamada T. The         filamentous phage XacF1 causes loss of virulence in Xanthomonas         axonopodis pv. citri, the causative agent of citrus canker         disease. Front Microbiol. 2014 Jul. 1;5:321.         Casadevall A, Day L A. DNA packing in the filamentous viruses         fd, Xf, Pf1 and Pf3. Nucleic Acids Res. 1982 Apr.         10;10(7):2467-81.         Chen F C, Koopmans G, Wiseman R L, Day L A, Swinney H L.         Dimensions of Xf virus from its rotational and translational         diffusion coefficients. Biochemistry. 1980 Apr. 1;19(7) :1373-6.         Cheng C M, Wang H J, Bau H J, Kuo T T. 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1. An isolated or recombinant nucleic acid molecule comprising a nucleotide sequence encoding an amino acid sequence, wherein said nucleotide sequence is selected from the group consisting of: a) the nucleotide sequence set forth in any of SEQ ID NO:1, 24, 25, 2 or full length complements thereof; and b) a nucleotide sequence having at least 90% sequence identity to SEQ ID NO: 1, 24, 25 or
 2. 2. The isolated or recombinant nucleic acid molecule of claim 1, wherein said consists of the sequence of SEQ ID NO:1 or its full length complement, or SEQ ID NO:24 or its full length complement, or SEQ ID NO:25 or its full length complement, or SEQ ID NO:2 or its full length complement.
 3. The isolated or recombinant nucleic acid molecule of claim 1, wherein said nucleic acid segment comprises a cDNA molecule.
 4. A vector comprising the isolated or recombinant nucleic acid of claim
 1. 5. The vector of claim 4, wherein said vector replicates in a Cf-type phage-infected Xanthomonas citri host.
 6. A host cell comprising the vector of claim 4, wherein said host cell is optionally a bacterial cell or plant cell.
 7. The host cell of claim 6, wherein said host cell is a bacterial cell and said bacterial cell is a Xanthomonas citri subsp. citri cell.
 8. A method of expressing a recombinant gene in a Cf-type phage-infected Xanthomonas citri cell comprising: (a) preparing a nucleic acid molecule comprising a recombinant gene fused with a sequence or in accordance with SEQ ID NO:1, 24, 25 or 2 which encodes the amino acid sequences comprising SEQ ID NO: 3-12, or SEQ ID NO: 27-52; (b) transforming said molecule into a uninfected or phage-infected bacterial cell; and (c) culturing said cell under conditions appropriate for the expression of said recombinant gene.
 9. A method of generating recombinant Cf-type phages that infect Xanthomonas citri cell comprising: (a) preparing a nucleic acid molecule comprising SEQ ID NO:1, 24, 25, 2 or one or more nucleotide are additions, deletions, or substitutions of SEQ ID NO: 1, 24, 25 or 2; (b) transforming said molecule into a uninfected or phage-infected bacterial cell; and (c) culturing said cell under conditions appropriate for the growth of recombinant phages.
 10. A method of generating recombinant and controllable Cf-type phages that infect Xanthomonas citri cell comprising: (a) preparing a nucleic acid molecule comprising SEQ ID NO:5, 32, or 44 or one or more amino acid additions, deletions, or substitutions of SEQ ID NO: 5, 32, or 44; (b) preparing a nucleic acid molecule comprising a X. citri gene fused with a sequence or in accordance with SEQ ID NO:1, 24, 25, to replace the nucleotide sequence that encodes the amino acid sequences containing SEQ ID 5, 32, 44; (c) transforming said molecules in (a) and (b) into a uninfected or phage-infected bacterial cell; and (d) culturing said cell under conditions appropriate for the growth of recombinant phages.
 11. A method of generating recombinant Cf-type phages that infect Xanthomonas citri cell with improved shelf life comprising: (a) preparing a nucleic acid molecule comprising a recombinant gene, which encodes the amino acid sequences containing SEQ ID 13-23, fused with a sequence or in accordance with SEQ ID NO:1, 24, or 25; (b) preparing a nucleic acid molecule comprising a gene sequence encoding SEQ ID NO:13-23 or one or more amino acid are additions, deletions, or substitutions of SEQ ID NO: 13-23; (c) preparing a nucleic acid molecule comprising a X. citri gene fused with a sequence or in accordance with SEQ ID NO:1, 24 or 25, to replace the nucleotide sequence that encodes the amino acid sequences containing SEQ ID 4, 30, or 45; (d) preparing a nucleic acid molecule comprising a sequence or in accordance with SEQ ID NO:1, 24, or 25 where one or more nucleotides are added, deleted, or substituted in nucleotides that encode the amino acid sequence in accordance with SEQ ID NO:4, 30, or 45; (e) transforming said molecules in (a), (b), (c) and (d) into a uninfected or phage-infected bacterial cell; and (f) culturing said cell under conditions appropriate for the growth of recombinant phages.
 12. A method of generating recombinant Cf-type phages that infect and kill Xanthomonas citri cell comprising the steps of: (a) preparing a nucleic acid molecule comprising a recombinant gene able to inhibit and kill X. citri fused with a sequence or in accordance with SEQ ID NO:1, 24, 25, or 2; (b) preparing a nucleic acid molecule comprising a gene sequence encoding SEQ ID NO:5, 32, or 44; or one or more amino acid additions, deletions, or substitutions of SEQ ID NO: 5, 32, or 44; (c) preparing a nucleic acid molecule comprising a recombinant gene able to inhibit and kill X. citri, and a X. citri gene fused with a sequence or in accordance with SEQ ID NO:1, 24, 25, to replace the nucleotide sequence that encodes the amino acid sequences containing SEQ ID 5, 32, 44; (d) transforming said molecules in (a), (b) and (c) into a uninfected or phage-infected bacterial cell; and (e) culturing said cell under conditions appropriate for the growth of recombinant phages.
 13. A method of generating recombinant Cf vectors and phages that can carry foreign genes and integrate into Xanthomonas citri host genome comprising: (a) preparing a nucleic acid molecule comprising a recombinant gene fused with a Cflt phage DNA sequence or in accordance with SEQ ID NO:1, 24, or 25, where one or more nucleotides are added, deleted, or substituted, to replace the nucleotide sequence that encodes the amino acid sequences containing SEQ ID 5, 32, or 44; (b) preparing a nucleic acid molecule comprising a gene sequence encoding SEQ ID NO:5, 32, or 44, where one or more nucleotides are added, deleted, or substituted; (c) transforming said molecules in (a) and (b) into a uninfected or phage-infected bacterial cell; and (d) culturing said cell under conditions appropriate for the growth of bacteria and recombinant phages.
 14. The method of claim 8, 9, 10, 11, 12 and 13, wherein said bacterial cell is a Xanthomonas citri subsp. citri cell.
 15. A method to purify Cf-type phage composition comprising Cf-type phages and variants (Cf1t, Cf1c, Cf1tv, Cf16, Cf16-tv1, Cf-tv2, XacF1, Cf2) and the recombinant Cf-type phages in claim 8-13.
 16. A phage composition comprising at least two bacteriophage isolates selected from the group consisting of claim
 15. 17. A method for preventing the growth of Xanthomonas citri subsp. citri microorganisms on a food product, plant cultivar, or gardening tools comprising: contacting said food product with a microbial growth inhibiting effective amount of a bacteriophage composition comprising Cf-type phages or variants (Cf1t, Cf1c, Cf1tv, Cf16, Cf16-tv1, Cf-tv2, XacF1, Cf2) or the recombinant Cf-type phages in claim 8-13, wherein the application time of said bacteriophage composition is for at least a fraction of a second to prevent the growth of microorganisms on the food product and plant cultivar.
 18. The method of claim 17, wherein said contact is by spraying, misting, dipping, or soaking.
 19. The method of claim 17, wherein the food product is selected from the group consisting of fruits and trees. Plant cultivar is grouping of plants selected for desirable characteristics that can be maintained by propagation. Gardening tools are selected from the group consisting of the tools in working environments for growing food and supply.
 20. An isolated or recombinant nucleic acid molecule comprising a contiguous sequence consisting of XP12 phage genome DNA.
 21. The isolated or recombinant nucleic acid of claim 20, wherein said nucleic acid segment comprises a cDNA molecule.
 22. A vector comprising the isolated or recombinant nucleic acid molecule of claim
 20. 23. The vector of claim 22, wherein said vector replicates in a XP12 phage-infected Xanthomonas oryzae host.
 24. A host cell comprising the vector of claim 22, wherein said host cell is optionally a plant or bacterial host cell.
 25. The host cell of claim 24, wherein said host cell is a bacterial host cell comprising a Xanthomonas oryzae cell.
 26. A method of generating recombinant XP12 variant phages that infect Xanthomonas oryzae cell comprising the steps of: (a) preparing a nucleic acid molecule comprising XP12 phage DNA, where one or more nucleotides are added, deleted, or substituted; (b) preparing a nucleic acid molecule comprising one or two gene sequences encoding XP12 essential proteins; (c) preparing a nucleic acid molecule comprising a recombinant X. oryzae gene fused with XP12 phage DNA, to replace the nucleotide sequence that encodes the amino acid sequences in (b); (d) transforming said molecules in (a), (b) and (c) into a uninfected or XP12-infected bacterial cell; and (e) culturing said cell under conditions appropriate for the growth of recombinant phages.
 27. The method of claim 26, wherein said bacterial cell comprises a Xanthomonas oryzae cell.
 28. An isolated or recombinant nucleic acid comprising a contiguous sequence consisting of Xf phage DNA sequence of SEQ ID NO:26 or its full length complement.
 29. The isolated or recombinant nucleic acid of claim 28, wherein said nucleic acid segment comprises a cDNA molecule.
 30. A vector comprising the isolated or recombinant nucleic acid of claim
 28. 31. The recombinant vector of claim 30, wherein said vector replicates in an Xf phage-infected Xanthomonas oryzae host.
 32. A bacterial cell containing the recombinant vector of claim
 31. 33. The bacterial cell of claim 32, wherein said cell is a Xanthomonas oryzae cell.
 34. A method of generating recombinant Xf variant phages that infect Xanthomonas oryzae cell comprising: (a) preparing a nucleic acid molecule comprising Xf DNA, in accordance with SEQ ID NO: 26, where one or more nucleotides are added, deleted, or substituted; (b) preparing a nucleic acid molecule comprising a gene sequence encoding amino acid sequence SEQ ID NO: 52-62, 13, or one or more amino acid additions, deletions, or substitutions of SEQ ID NO: 52-62; 13, (c) preparing a nucleic acid molecule comprising a recombinant X. oryzae gene fused with Xf DNA, to replace the nucleotide sequence that encodes the amino acid sequences SEQ ID NO: 52-62; 13, (d) transforming said molecules in (a), (b) and (c) into a uninfected or Xf-infected bacterial cell; and (e) culturing said cell under conditions appropriate for the growth of recombinant phages.
 35. The method of claim 34 wherein said bacterial cell is a Xanthomonas oryzae cell.
 36. A method to purify XP12 and Xf phages in claim 26 and
 34. 37. A phage composition comprising at least two bacteriophage isolates selected from the group consisting of claim 24 and
 34. 38. A method for preventing the growth of Xanthomonas oryzae microorganisms on a food product or gardening tools comprising: contacting said food product and plant cultivar with a microbial growth inhibiting effective amount of a phage composition comprising the XP12, Xf phages, or recombinant phages in claim 24, 24 or 37, wherein the application time of said bacteriophage composition is for at least a fraction of a second to prevent the growth of microorganisms on the food product and plant cultivar.
 39. The method of claim 38, wherein said contact is by spraying, misting, dipping, or soaking.
 40. The method of claim 38, wherein the food product is selected from the group consisting of fruits and trees. 